Might want to check Grav out again. Animation times got reduced (either in I5 or I6, I forget which) and Wormhole's stun got better in I6 as well.
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Storm is really close range, but I do like the ability to grab mobs with Wormhole, and throw them all in a corner so that I can use Hurricane to pin them there.
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Hurricane plus lightning storm! That storm has considerable knockback, though it's one target at a time and you can't predict who it will hit. If you really want to get mean, re-summon the Singularity near the corner as well to do repel and throw in some holds/immobilizes. Oh, and don't forget the slow/knockdown of freezing rain!
Storm is a wicked corner power and Grav's Wormhole makes using corners fun and easy.
Great idea! And a big help to new controllers /em doffing hat
Relating specifically to Mind/ it's important to keep in ahem... mind... the tremenous single target control abilities that Mind brings to the table. Mind can not only layout more single target damage mitigation faster than anyone else (all out of the primary), but with the stacking of Dom, TD and TK it's the only set I know that can effectively hold an elite boss right out of the gate. Mind/Kin REALLY shines in the late game where Mass Hyp gives you alpha free access to all of FS glorious damage boost every combat. And Transfusion + Transferance -> immediate return to full bars if anything goes wrong. Mind and Kin have excellent synergy, though pretty much ANY secondary is great with Mind, all in different ways. Mind doesn't get much soft control because, frankly, it doesn't need it much. Though Obviously I'm not exactly impartial... 
Yeah....what he said! Mind Kin has some great synnergy. It one of the few Primaries that has an AoE damage power to take advantage of Fulcrum Shift and Siphon Power.
Not saying that single target doesn't benefit from them, just that....AoE.....crap.....you know what I mean!!
Great idea - as others have mentioned there are some fantastic synergies between Mind and Kin (although Mind can launch controls from range it by no means has to remain at range - in fact it is one of the safest primaries to be in melee with).
Also, I'd point out some of the really nice synergy between Fire and Sonic - the debuff anchor on the melee pets, the +Res shields for the normally squishy pets, and the overall damage increase from the two debuffs. Plus an additional AoE location control (that you point out Fire is lacking) is sitting right there at Tier 9 in Liquefy.
But yeah, excellent idea and nice work 
ICE/STORM is actually very complementary. The only powers that don't really work together are Hurricane and Arctic Air. (Frostbite and ice Slick are not complementary either, but both of them are from the ICE set, so no avoiding that no matter what secondary you choose.) Arctic Air is a great power, if you want/need to get in close, but.......
ICE/STORM has great ranged powers, and those powers work great with the PBAoE defensive powers.
It is a offensively weak power set until you get to the mid 30s, but it is great in PuGs, not to mention regular teams. Ice Slick, Ice Storm, Block of Ice and Chilblain are all great pre-20 powers that can help any team, no matter the foe. Ice Storm and Ice Slick are effectively a ranged AoE Hold available every fight (or more, if the fight lasts for more then a minute). I don't take Glacier (and don't miss it) because of the effectiveness of the Slick/Storm combo. Shiver is almost overkill for flooring the mob's move speeds and recharge times.
Hurricane and Steamy Mist make a great combo. Blasters and other squishies can sit safely in the melee free zone while blasting and controlling away. If you don't move around like a caffeinated squirrel, people start to use the Hurricane/Steamy Mist area to their advantage.
Steamy mist helps keep sniping Blasters unnoticed, and myself safe while traveling in PvP zones.
In melee heavy teams, I'll park myself just so the edge of the Hurricane is touching the mobs while the Steamy Mist is giving the Tank the extra fire/cold/energy damage resistance he needs to blow off any incoming elemental hits.
When the 32+ levels finally arrive, your ability to start adding to the damage output becomes increasing realized. Tornado can cause an ungodly mess, but with Chilblain placed upon a mob that doesn't get tossed away, it just sits and tears through mobs like nothing. Toss Lighting Storm into the mix, and it's like the Wrath of God coming down on you.
With Stamina 3 slotted, I can keep Hover, Hurricane, Steamy Mist, Assault and Tactics up indefinitely. Start tossing powers around and I will run low before the fight is over, but with Hover off OR with Recovery Aura/Speed Boost, END is not an issue.
An ICE/STORM can solo, but it really shines in a team setting. No matter what, it always looks great!
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Great idea - as others have mentioned there are some fantastic synergies between Mind and Kin (although Mind can launch controls from range it by no means has to remain at range - in fact it is one of the safest primaries to be in melee with).
Also, I'd point out some of the really nice synergy between Fire and Sonic - the debuff anchor on the melee pets, the +Res shields for the normally squishy pets, and the overall damage increase from the two debuffs. Plus an additional AoE location control (that you point out Fire is lacking) is sitting right there at Tier 9 in Liquefy.
But yeah, excellent idea and nice work
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A lot of that applies to Illusion as well. You can put the team-anchored sonic debuff on the Phantom Army, and sonic provides a couple nice complements to Illusion.
Cool guide, but I'd write the same guide from the opposite perspective. You generally focus on filling the gaps and holes in primaries with abilities from the secondary. I tend to focus on powers that give escalating synergies - who cares about the holes in the build if your strong points are really strong?
This is not a guide proper, merely some observations I've made and some builds I'm playing.
Earth Control
Agree storm works best here, and my earth controller is storm. But I think Rad7Choking Cloud ought to mesh very well with Quicksand because of the -Acc.
Fire Control
My Fire controller is Trick Arrow. Hot Feet automatically ignites Oil Slick with no extra effort. This makes my damage very nice indeed. Trick Arrow is a dark horse; the added single-target control makes boss holing a breeze, and things like Glue Arrow are a great boon indeed.
Ice Control
I have a lvl 50 Ice/Kin, which is not bad, but is seriously lacking in synergies. Arctic Air is good, but draws plenty of aggro. By level 30, you are almost guaranteed to get mezed when using it. The way around this is to get Sonic or Force Field. But I generally find Ice a little lacking - the lack of alpha mitigation hurts the set badly.
Gravity Control
I want to like this set, but I've failed so far.
Illusion Control
Illusion is a very nice set but has few synergies that I can see.
Mind Control
My mind is a sonic. Sonic Siphon (the first power) has a reasonably fast recharge ad works decently as a part of an attack chain with Mind's single-target powers, giving you a decent-damage single-target attack chain. But the synergy is not really startling.
Continuing the series discussing the synergies between primaries and secondaries within each AT. This is not about thematic synergy (AR/Dev), nor is it about pairing each primary with the best secondary. It's about which sets has more of its abilities become especially useful when paired with another particular set.
Now discussing: Controllers.
Prior: Blasters
Earth Control :
Earth Control is a heavy control set, with location-targeted controls and debuffs. The pet is a tanker pet, relatively slow and hard to kill. The powers that separate the set from others are Quicksand (area-targeted -Slow, -Jump, -Fly, -Def) and Volcanic Gases (area-targeted pulsating Hold). Also, almost all powers have a solid -Def component to them.
Due to having several location-based powers (Quicksand, Volcanic Gases, Earthquake), Earth benefits from a secondary that will help it reposition the mobs, and that will help it prevent mobs from leaving the areas. Due to having a slow tough pet, Earth will benefit from having a secondary that buffs the pet's offense, and from having a ranged heal. Empathy is good for the pet but helps nothing with positioning. Rad, while a good set overall, only provides Lingering Radiation unless the caster is willing to run in with Choking Cloud in order to draw mobs into the target area. TA has nice overlap with Oil Slick and Glue Arrow, but doesn't help the pet at all (though he doesn't need it). And FF helps Stoney tank, which isn't all that necessary, but while it can push mobs into position, it does nothing to slow them. My choice would be Storm, as Hurricane can push mobs into the zone. When there, it will debuff their accuracy, while Earth's powers debuff their defense. Snow Storm and Freezing Rain slow them down and keep them in the location, while adding more knockdown. Tornado is a more situational power, unfortunately, but the rest of Storm works very well with Earth. Kinetics and Radiation also work well, but don't multiply the power effects with the primary as much as Earth/Storm.
Fire Control :
Fire Control lacks, for the most part, area-targeted powers. Its AoE Hold is PBAoE, and it has a major damage power (Hot Feet) that is PBAoE, and that benefits from Containment. Since using Hot Feet with Flashfire (Disorient) is subject to mobs wandering out of range, many Fire Controllers will use Fire Cages to prevent mob wander. For them, this makes sense since they do not have a pulsing Knockdown power that will be negated by an Immobilize. For these reasons, Fire Controllers are often in point-blank range. Their pets do heavy damage but are relatively vulnerable, and due to being summoned in threes, benefit from AoE healing powers.
At this point, there are really only two sets to consider: Radiation and Kinetics. Rad's debuffs help in survival at close range, Lingering Radiation adds a -Slow that stacks with Hot Feet to approximate an Immobilize, and AM can buff all three Imps at once. However, Speed Boost and Increase Density can be reasonably maintained on the Imps, and Kinetics works very well in melee range. Hopefully a controller can manage to control the mobs so that he is relatively safe, thus negating Rad's main advantage (defensive debuffs). And, offensively, there is nothing to compare to a Fulcrum Shifted controller using Hot Feet with Containment, with three FS'd Fire Imps next to him. Thus, I consider Kinetics the best secondary, and Radiation as good alternate.
Ice Control:
Ice Control is very similar to Earth. The associated debuff is -Recharge rather than -Defense. Also, its ranged debuff is a click -Slow/-Recharge cone rather than Quicksand. It has a PBAoE debuff/confuse aura rather than a ranged Stun, and its AoE Hold is PBAoE. It only has one location power (Ice Slick), and it has two PBAoE powers (Glacier, Arctic Air). Thus, it is partially between Earth and Fire, in terms of being ranged vs PB, and target-centric vs location-centric.
Like Earth, it will benefit from Storm's ability to position mobs onto Ice Slick, and from the ability to stack Ice Slick with Freezing Rain and Snow Storm. Add in Arctic Air and/or Shiver, and mobs will be stuck in the Ice Slick, effectively immobile, with lowered recharged, and falling down. However, the problem is that Ice wants mobs around it to get effect out of Arctic Air/Glacier, which is not compatible with Hurricane. Like Fire, being used to going in the middle of mobs, it will benefit from Kinetics heals and Transference, but since it doesn't have an equivalent of Hot Feet or pets that do as much damage, it doesn't get the same benefit from Fulcrum Shift and Siphon Power. At this point, I'd be satisfied with either Storm or Kinetics, but neither really catches my eye. However, Radiation does. Ice kills more slowly than Fire, thus it needs to be safe for a longer period of time, and Arctic Air works well with Choking Cloud (if you can run both) to neutralize mobs around you. An Ice/Rad running onto Ice Slick with CC and AA active, ready to fire Glacier, and using Radiation Infection for safety, is a very safe controller. Thus, I really see Rad as the secondary of choice.
As a side note, I don't see Trick Arrows as really matching up especially well in general with any set, but sometimes what you want is just to fill in a particular hole. Well, both Ice and Earth lack damage output. Also, both have means of keeping mobs in a location due to knockdowns, slows, and ranged immobilizes. Therefore, both have need for AoE damage, and can keep mobs flopping in a location... which brings us up to Oil Slick Arrow. It is a very good AoE damage power from a secondary, which exactly fills in the biggest hole for Ice and Earth. Additionally, Flash Arrow provides a -Pcp/-Acc debuff that both Ice and Earth lack. And both Ice and Earth can keep mobs in one location to take best advantage of Disruption Arrow and Poison Gas arrow. Thus, while TA is subpar and I can't really recommend it for any set, if you're satisfied with using mostly your primary and just want the secondary to fill in the biggest holes, TA will do that nicely for Ice and Earth.
Gravity Control:
Gravity Control suffers from a lack of defining strengths. Its unique attributes (Wormhole's ability to reposition mobs, extra single-target damage powers, AoE enemy phase shift) aren't impressive enough to make up for some particular lacks (long animation times, only one secondary control power with poor duration/recharge). Thematics aside, the only real advantage of Gravity is Singularity, a superb tanking/control pet. At least it is all ranged.
Now, what do we want as a secondary with Gravity? First, I'd like something that provides control, preferably AoE control. Gravity does have enough single-target control that I'm not worried about that (so Kinetics' single-target debuffs/drains aren't useful). It's also all-ranged, so I figure to take advantage of one of its few strengths. At this point I'm looking at Rad and Storm for the control powers, and at TA for the all-ranged option. Storm is really close range, but I do like the ability to grab mobs with Wormhole, and throw them all in a corner so that I can use Hurricane to pin them there. Rad doesn't have to be melee unless we depend on Choking Cloud, since EMP has enough range to use from the outside of a fight. And TA can alternate its own debuffs with Gravity's controls, keeping the controller active in each fight. I would put Rad in first place due to CC plus EMP as fill-in control options, and TA in second due to the ability to remain all-ranged.
Illusion Control:
Illusion is a very different control set. It lacks Disorient and Immobilize and AoE mob debuffs, and instead has a AoE Fear power and two +Def/+Stealth self/group buffs. It also has Phantom Army, a unique aggro-control power, and has a pet with good single-target damage and great AoE damage. What Illusion lacks is direct damage (it has the fewest powers that cause or benefit from Containment), and any ability to control the movement of mobs by Immobilizes or Slows.
Phantom Army doesn't benefit from buffs, so a set that debuffs the enemy would be helpful. With PA to draw the alpha, and with good Invisibility powers, the Illusionist can enter melee range if they want, but other than to fire Flash, they have no reason to remain there. Thus, I like a ranged set, preferably with extra control options. This is leaving me with Rad and TA. Also Storm, since Illusion really lacks any ability to control mob movement and Storm has FR, Snow Storm, and Hurricane for that. Plus Thunderclap for extra control.
Out of the three, I'm putting TA in the back. TA's long recharges work well as "alternates", but Illusion doesn't really need "alternates". Its main soft controls (PA and Spectral Terror) are available every combat, while Flash doesn't see as much use as most other AoE Holds. So TA's ability to help every other combat may work with Gravity, but Illusion wants more of some additional every-combat help. Storm and Rad both work well, Storm for the ability to slow mobs, knock them down, push them around, and Rad for the every-combat debuffs. Rad is less affected by Phantasm's tendency to toss everything around, and Illusion draws less direct aggro than other sets so it gets less effect out of Hurricane's powerful defense. So I see Radiation as the best primary for Illusion, followed by Storm and TA.
Mind Control:
Mind Control is rather different. The most obvious difference is that it gets no pets. A less obvious is that it has no tools to control mob movement other than the Holds, which control everything. And, lastly, it doesn't prevent knockback in any way. This can be both good and bad. Mostly bad. Another difference is that it has a nice cone AoE damage power (Terrify), and thus would benefit from a quick easy method of creating Containment... such as an AoE Immobilize. Which it lacks. It has lots of control, both single-target and AoE, and all of the control is ranged. Lastly and most subtly, it lacks debuffs.
Debuffing and soft control powers are a major tool that Mind Control sacrifices for hard control. But usually, soft control and debuffs make up for their lesser effect, by being available every combat. So I would look for the secondary to have these powers.
Kinetics doesn't take advantage of Mind's ranged ability. They have to get in close for full effect. It's workable with MC since MC provides enough control to do this, but it doesn't really take advantage. Rad, assuming you skip Choking Cloud, is all ranged, and has nice debuffs. It's a pretty good match, especially with MC's Mass Hypnosis, since the Rad debuffs normally draw aggro but won't wake up sleeping mobs. So it's quite possible to open up with Terrify... upon mobs that are sleeping (for double damage) and debuffed by all three of Rad's debuffs. A very nice combination. Trick Arrow's Glue and Oil Slick provide soft control that MC lacks, and it's all ranged. Lastly, Storm provides mob positioning and debuffs that MC lacks, plus damage powers to make up for the lack of a pet when soloing. All of the debuff sets work well with Mind Control, but I like the ability to chain the AoE Sleep with Rad's debuffs in order to have all of the mobs debuffed without drawing aggro. Rad would be the choice of secondary here, followed by TA then Storm.
Some Final Notes :
Looking back, I've pretty much ignored the "buffing" sets in the secondaries. FF, Sonics, Empathy. The reason is that these sets gain their synergy more from their interaction with other teammates, rather than from their interaction with the primary. The primary set function, Control, is enemy-oriented. So are the secondary sets that Debuff. A secondary set that Buffs is ally-oriented. So it's very hard to see important synergies between an enemy-oriented set and an ally-oriented set.
FF can provide mob repositioning, so you should consider that... but I can't consider it as a better set for repositioning than Storm. Empathy is a good set to buff your pets, but since Kinetics will do that and also buff the caster, if your primary would benefit from having your pets boosted... I'd again go with Kinetics. Thus, if you're only looking at your own powersets for synergies, you won't find much between a Control set and a Buffing set.
If you are looking at taking a buffing set anyhow since you want to be better able to support your team, consider the following:
FF is an all-defensive buff set. Sonic is mostly defensive, though it adds -Res debuffs. Empathy is a mix between offensive and defensive, and Kinetics is almost all offensive.
So, consider the primary's ability to provide defense and/or offense. Earth Control will provide an offense boost since they have AoE powers with -Def. Earth and Ice also are good for offense since they have location-centered powers that will keep mobs grouped for AoEs. Mind Control is heavy on the defense, with their ability to control multiple spawns. So I wouldn't really pair up MC with FF or Sonics, while MC/Emp or MC/Kin would work in a team. Illusion is all defensive, since it has no offensive boosting, so again I'd skip FF or Sonics with it. Gravity has a slight offensive boost with the ability to reposition a spawn so it can be better attacked, but it's pretty minor. However, they do a serious amount of single-target damage if you don't have an active secondary, so you might get some use out of a "buff and forget" secondary like FF.