I don't know why this is complex. Take your pets and your upgrades. Done.
Secondaries are more of a matter of preference. Why didn't you like /Dark or /Poison? Personally I've tried both. /Dark I like, but my Corruptor does it better so I when the Corruptor route. /Poison is too single target and fiddly for me, so I don't care for it.
/Traps and /Dark have a rep for being decent, active secondaries. /Pain matures late but should be good on teams. But if you don't like the MM play style, maybe it's not for you. Brutes are fun too, and Corruptors are blastery. Doms are getting a buff soon.
I don't play Defenders or Doms, so not every class is for everyone. Just go with what's fun.
My opinion of the secondaries:
Dark has great debuffs and control plus a heal, good for boosting survivability of squishy pets or making tough ones nearly unkillable.
Force Field is fantastic for boosting survivability and for tanking, but the lack of debuffs makes for long, slow (but safe) fights.
Pain is best with tough pets, since squishy ones (like Ninjas) can die too fast to heal them. Suppress Pain plus Bodyguard is great for tanking though, so you can go that route to keep the pets alive.
Poison is great for soloing AVs but lousy on teams. It's full of powerful single target debuffs, so it doesn't do well against groups but it wrecks single targets. Goes well with Thugs since Noxious Gas is practically made for the Bruiser.
Storm is a great set for adding damage and keeping the pets alive. Hard to play well, but devastating if you get the hang of it. Probably one of the best sets for soloing.
Traps is probably the best tanking secondary. You get defense and status protection like Force Field, but you also get debuffs and an AoE regen buff for tough fights. Pair it with Bots for insane personal defense if you want to tank, or with Thugs to produce untouchable high-damage pets (not that Bot damage is bad either post-32).
Trick Arrow has nice debuffs but their recharge is a bit long. Works best with good global recharge, though you can just alternate between debuffs on every other spawn since dumping them all on one group is usually overkill. I personally prefer Dark or Storm for debuffing and Traps for general use, but some people swear by TA.
One simple rule to keep in mind... buff sets work best with ranged pets that will stay grouped up in the buff radius, while debuff sets are a better choice if you use melee pets. The best way to keep Ninjas alive is to use Dark or Storm to insure that everything is either terrified, knocked down, or debuffed into the middle of next week. The best way to keep Bots alive is... don't go AFK in the middle of a fight if the enemies are more than +2s. Unless you're Bots/FF, then you can go AFK on +3s just fine. 
Cascade, level 50 Blaster (NRG/NRG since before it was cool)
Mechmeister, level 50 Bots / Traps MM
FAR too many non-50 alts to name
[u]Arcs[u]
The Scavenger Hunt: 187076
The Instant Lair Delivery Service: 206636
Thanks! That's exactly what I wanted, I'd love one of the primaries too.
I'm also very curious as to why people seem to hate Mercs.
My take on MM primaries:
Mercs are probably the weakest set, but that doesn't mean they are worthless. Mercs are all ranged attackers so they tend to be easy to control and you can keep them gathered up within buff / heal range. However, they do Lethal damage, which is heavily resisted, and don't really have anything special going for them other than some controls (stuns and immobilizes) that are on very long timers. Well, they do get a Medic that can heal, but he's not that great at it. Mercs can be good once you IO them out, but you need Achilles' Heel procs in the pets to make up for their heavily resisted damage type.
Necromancy is the control set. Most of the pets are melee, so they're a bit harder to manage, but they have self heals and debuffs so they can take care of themselves somewhat. The Lich is almost a pocket Controller... it uses holds and fear powers as well as accuracy debuffs. Soul Extraction summons a temporary pet with even more debuffs and controls. Necro / Dark is such a powerful debuffing combo it makes Dark / Dark Defenders jealous.
Ninjas deal tons of single target damage but tend to die if you look at them funny. They're great paired with a heavy debuffing secondary that can actually keep them alive, but are otherwise squishy. They are also by far the hardest pets to manage, since they are not only melee, but also have enhanced running speed. Your ninjas can and will run off and aggro another group two hundred feet away if you aren't careful, and they're so fast they can do so in a couple of seconds. They do hit very hard if you learn how to handle them though.
Bots are slow starters but extremely powerful late game. They do mostly Energy damage, which is one of the least resisted types. They are also very tough, since they have some innate resistances and the Protector Bots can heal and have bubbles that act like both Force Field bubbles combined. Slot the Protectors with a couple of Defense SOs and they give about 12% defense per bubble... which is 12% on you, 12% on the Protectors, and 24% on the Assault Bot and Drones. Bots are slow at low levels since they have no AoEs, but once you get the Assault Bot they speed up a bit. Then you hit 32, get the second upgrade, and suddenly all of the bots have powerful AoE attacks that do Energy or Fire damage. After that they tear spawns to shreds. Since the Protector Bots will also bubble the Mastermind, Bots are the best primary for Tankerminds... pair them with Force Fields or Traps and you can soft-cap your personal defense with decent IO slotting. Those sets can also soft-cap the Bots' defense if you add a defense aura IO and Maneuvers.
Thugs are a bit squishier than Bots but even more damaging. They get AoEs earlier, and even though they do a lot of Lethal damage they do so much of it that the higher resists don't matter as much. They also get the Arsonist, who does massive Fire damage over an area (and also dies a lot from all the aggro). The fun thing about Thugs is that two of their pets actually have class abilities. The Arsonist is a Corruptor, so his attacks can Scourge. The Bruiser is a Brute, so he gets Fury and has resistances. He also does Smashing damage and gets Foot Stomp, so Thugs have three different damage types well represented. Finally, the Enforcers get Leadership powers that enhance accuracy, defense, and damage on all nearby Thugs, even those belonging to other Masterminds. Thugs get Gang War, which summons a horde of weak minions that do minimal damage but generate a lot of aggro and tend to distract the enemy... and Gang War accepts Recharge Intensive Pet sets as well as normal pet sets. That means you can slot both sets of resist and defense auras in it! If you take Traps or Force Fields and use both defense auras you can have your whole horde of Thugs with soft-capped defense, and Dark or Storm can do effectively the same thing by debuffing enemy accuracy. Oh, and Thugs gives you dual pistols... can't forget the dual pistols.
Overall, I love Bots and Thugs. Especially Bots, though that's as much for aesthetic reasons as anything else... killer robots are cooler than gang members. Laser rifles are also cooler than dual pistols to me. If you want a strong, easy to use set I'd play one of those two. Mercs are also easy to use since they're all ranged, but they're not as strong. It's not so much that Mercs are that bad, it's more that Bots and Thugs are that good. Melee pets are harder to use and take more practice, especially Ninjas. Though if you really like Controllers I'd say try Necro / Dark... the sheer amount of debuffing and fear that combo puts out is incredible.
Cascade, level 50 Blaster (NRG/NRG since before it was cool)
Mechmeister, level 50 Bots / Traps MM
FAR too many non-50 alts to name
[u]Arcs[u]
The Scavenger Hunt: 187076
The Instant Lair Delivery Service: 206636
you pretty much hit the nail on the head.
although the lethal resistance isnt THAT bad really. sure its resisted alot but its not like 50% lethal resistance or even 33%.
My take on bots is that there are so many little things that get to me that it all adds up into 1. I like to play with the sound on, thus i here the freaking stomping of 6 robots ALL the time! also the PEW PEW is rather annoying once you get the second upgrade (the battle drones have that stupid full auto laser..ugh). The Bigbot as i call it is the only real damage dealing pet. sure the protecters deal some damage but are probably the lowest second tier pet when it comes to damage.
The worst thing is the Incindiary rounds on the Bigbot. It causes a mag 50 Fear that makes enemies run. ussually this isnt a problem but when your on relentless you dont want a purple boss running away because your bots will start chasing it and yada yada yada. Also i was Robot/Traps so keeping the enemy near my Acid mortar and Poison Trap is very important (poison trap for AVs only really). All the knockback and Fear makes the enemies move around too much for your poison trap to go off and ocassionally move them out of the acid mortar.
But this is all with Robots/Traps. Other than that its almost unstoppable. I never had to resummon my robots during an AV fight, it was just extremely frustrating when the AV moves away from your poison trap or when the Mag 50 Fear makes the enemies run far far away closer to another group.
Thugs though is much more fun for me so far. no clankity-clank-clank. No PEW PEW. Sure i get a suicidal Pyromaniac but its a fair trade for the Bruiser and the Enforcers. Also the Enforcer's leadership powers stack so you get a very hefty defense bonus.
So for my personal taste and take: Thugs > Robots
Whining about everything since 2006.
Ammo switching for Dual Pistols was my idea:
http://boards.cityofheroes.com/showthread.php?t=135484
In this game, you never need a spreadsheet. Especially with Masterminds. All of the sets will turn you into a steamroller before you know it. Relax.
lethal resists really arent a big issue if you take a secondary with some resistance debuffs. the problem with mercs is not just the lethal resists, but the tiny yet fast ticking dots they use (and really long recharges they shouldnt have anymore) PLUS the resists.
thugs is mostly lethal and smashing dmg, and doesnt have a dmg problem at all. this is because it's the one-two combo of having short burst-high dmg per tick dot cones and having them also recharge very fast. i've also found it easier to keep the achille's heal proc up on thugs enforcers than any of the merc pets. probably because the enforcers NEVER STOP shooting. the mercs will pause on occasion
The Assault Bot's incindiary missiles do scatter enemies, but it's really no big deal on anything under a boss. With bosses or higher, you do want to keep them in the patch for best results... but fortunately MMs have ways to do so.
<ul type="square">[*]Web Grenade in Traps (well slotted it can immobilize an elite boss or AV through a Dispersion Bubble)[*]Slows like Caltrops, Tar Patch, and Snow Storm[*]Repels and knockback if a corner is handy and the target isn't immune[*]Patron immobilizes, especially the one in Mu since it has -KB. Well slotted they'll stack to immobilize a boss or AV.[/list]
One reason Bots pair so well with Traps is the fact that Poison Gas and Caltrops will keep a spawn in the incindiary missile fire patches a lot longer, while Web Grenade insures that hard targets never move at all. Fully slotted with Trap of the Hunter it can be stacked six times, more than enough to perma-immobilize just about anything except some custom AE critters, while giving you some nice set bonuses and a damage proc. And if you can't immobilize it, just set the Bots to Stay and they won't chase after it... it'll be back once it runs out of the patch and while it's running around in fear it's not shooting you.
As for the clanking and "pew pew pew" sounds, that's part of what I like about the Bots, so it's all a matter of taste.
Cascade, level 50 Blaster (NRG/NRG since before it was cool)
Mechmeister, level 50 Bots / Traps MM
FAR too many non-50 alts to name
[u]Arcs[u]
The Scavenger Hunt: 187076
The Instant Lair Delivery Service: 206636
I was hoping somewhere in there would be like a spreadsheet or google doc with what are the benefits and the draw backs of each primary, in and of themselves. What are the benefits and drawbacks of each secondary in and of themselves and why some things mesh well, while others don't.
I was hoping that because MM's are so complex that someone would have done this already.
I am sad I am wrong. I've tried making masterminds before, I even went through and key bound all the crap, but both of my masterminds were Merc/dark or Bots/Poison, and I hated them around level 14 and deleted them.
Is there anything like this floating around?