The first thing to remember is the Stalker power sets are very tight and you dont really want to spend your power slots on anything not essential. Taking TP Friend is ok if you are then going for TP as your primary travel power but tp uses loads of end so prepare to slot it havily if you do.
By themsaelves Hover and Fly arent particularly suited to melee fighters on their own outside of PvP and are more suited to those that rely on range.
Superspeed is a good option with a choice of Hasten or Flurry as the initial must have power. Hasten is very useful if you are a regen and flurry is great if you want an additional attack without wasting a slot.It's also a fast travel power.
Superjumping is another good one with one of the initial powers being combat jumping which is very useful for defense and later on Acrobatics which is another useful power if you opt for it.It is also a fast travel power.
Out of the 4 as a stalker I would opt for either ss or sj as your travel powers as both have the greatest advantages for a melee fighter.
My thoughts on best travel power:
For PVE
For getting to and from missions it doesn't really matter.
Teleport takes some getting used to at first and does consume energy more than the others. It's also harder to use to run away when things go pear shaped in indoor missions due to camera angles.
I'm led to believe that superjump isn't great for escaping on indoor missions.
Fly can be a bit slow escaping indoors, especially in long corridors.
Super Speed is great for escaping with!
For PVP:
My experience is that 99% of blasters, controllers & defenders hover. Permanently. They think it makes them safe from melee villains. For a martial arts stalker it could do as you don't have a ranged attack (as far as I'm aware).
Sneaking up behind unsuspecting flying heroes can be quite satisfying if you've got fly (I had the jingle jet). Fly/hover is the only way you'd get an assassin's strike in against a flying hero.
You could launch normal attacks on them with Superjump by queing the attack and jumping into range. Similarly you could teleport next to them and launch the attack as you fall (this is proving lots of fun for me at the moment 
however I suspect it's quite hard with only melee range attacks.
With super speed you could wave at them from the ground.
Alternatively if you took tp foe instead of tp friend you could tp them next to you before attacking.
For the all important stalker pvp tactic of 'run away!' I find teleport is fantastic. I believe super jump is good as well. Not seen anyone use super speed to do so and confirm that a jingle jet (flying) is absolutely useless.
Speed Pool:
Flurry, poor attack, not status effect, not worth it.
Hasten, great power, whilst active all your powers recharge faster, so you can have Build Up and Placate up more often.
Superspeed, cheap fast movement with added stealth in PvE. The best in mission travel power and also the fastest. Unfortunately you have to get to know the zones because of the lack of vertical movement.
Jumping Pool:
Jump Kick, poor attack again I think.
Combat Jumping, cheap jumping power, adds great air maneuverability and allows you to change direction mid jump. Good for jumping over Mastermind pets. Also adds a miniscule amount of defence that will stack with your secondary. Provides protection against immobolisation.
Super Jump, cheap fast jump movement, slower than superspeed but provides vertical movement. Can be tricky to control.
Acrobatics, provides Hold and Knockback protection. However only Ninjitsu stalkers do not have Knockback protection so this will be unnecessary for you.
Flight
Air Superiority, good attack as far as I've heard, not for the damage but for the -fly and guaranteed knockdown. Keeping an enemy on the floor means he cannot attack you.
Hover, super slow speed flight, useless for a melee character.
Fly, endurance expensive flight. This is the slowest travel power, however it is the most versatile. You can usually cross a zone before running out of endurance. It needs to be slotted to reach its full potential.
Teleport
Recall Friend, very useful, has effectively infinite range, pretty cheap, nice power.
Recall Foe, can be used to teleport enemies to you, it can fail, I don't think it is that useful.
Teleport, the most irritating travel power, it is the fastest if slotted but is an endurance hog. You need to click on the place to teleport, you then have 2 seconds of hovering to activate teleport again and then choose the next destination.
Personally I think Superspeed is the best, however most people prefer Flight or Superjump.
@Unthing ... Mostly on Union.
Thank you all for your replies, i have some thinking to do now. I was pretty sure i didnt want fly as i have other characters with fly. I also have one character with ss and spend a lot of time running into buildings but i think if i got used to it could prove very useful. Time to weigh it all up me thinks 
Also should i be going down the fitness pool route, i have no idea what the stamina is like for stalkers, or is that something only to consider later on at the higher levels?
My */EA stalker survived to l30 without stamina.
He did it by thinking about which toggles needed to be up and only using the necessary toggles. In PVE it was painful but do-able. In PVP it was a pain in the backside.
The two earlier powers in the fitness pool (swift & health) came much earlier as I wanted to not need to use sprint, also had a power which had a speed penalty and wanted the quicker healing rate for survivability.
Best advice is to decide for yourself whether your play style needs it.
In PVP TP is a great get out of jail free card, though I personally dont like it.
I use Fly and SS combined on my PVP build and it rules
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In PVP TP is a great get out of jail free card, though I personally dont like it.
I use Fly and SS combined on my PVP build and it rules
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I assume you have hover (for AS-ing flying enemies). How fast is Hover with SS?
Personally i would take air superiority over hover for pvp.
Hover isnt affected by SS.
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In PVP TP is a great get out of jail free card, though I personally dont like it.
I use Fly and SS combined on my PVP build and it rules
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I assume you have hover (for AS-ing flying enemies). How fast is Hover with SS?
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Nope fly as well, hover sucks as SS doesnt affect it, the 3D escape route is v useful at times too 
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I woldnt recommend a multi travel build until you at least get to 40. PvP for a stalker is very different fron PvE with a stalker.
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I assume you have hover (for AS-ing flying enemies). How fast is Hover with SS?
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Nope fly as well, hover sucks as SS doesnt affect it, the 3D escape route is v useful at times too
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Well, that's odd. It must make AS-ing flying foes difficult, due to fly's inertia, and also quite an end-drain.
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I assume you have hover (for AS-ing flying enemies). How fast is Hover with SS?
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Nope fly as well, hover sucks as SS doesnt affect it, the 3D escape route is v useful at times too
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Well, that's odd. It must make AS-ing flying foes difficult, due to fly's inertia, and also quite an end-drain.
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I woldnt recommend a multi travel build until you at least get to 40. PvP for a stalker is very different fron PvE with a stalker.
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Its the cornerstone of my specific PVP build thats why end draining toggles have been dropped, its also vital on my storm troller killing runs to get out of line of sight when impaling. As I said before my build is quite unusual and specialised As has been said I wouldnt recommend it for a PVE build
as for ASing flying foes, I guess Im experienced with it now as if they in the air they going down
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Its the cornerstone of my specific PVP build thats why end draining toggles have been dropped, its also vital on my storm troller killing runs to get out of line of sight when impaling. As I said before my build is quite unusual and specialised As has been said I wouldnt recommend it for a PVE build
as for ASing flying foes, I guess Im experienced with it now as if they in the air they going down
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With regard to end drain... AFAIR from my corruptor, Fly is VERY end hungry, toggles or not. I found that any attempt to fight in the air (with fly instead of hover turned on) ended quickly with me running for end (PvE wise, I don't PvP with that corruptor).
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Its the cornerstone of my specific PVP build thats why end draining toggles have been dropped, its also vital on my storm troller killing runs to get out of line of sight when impaling. As I said before my build is quite unusual and specialised As has been said I wouldnt recommend it for a PVE build
as for ASing flying foes, I guess Im experienced with it now as if they in the air they going down
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With regard to end drain... AFAIR from my corruptor, Fly is VERY end hungry, toggles or not. I found that any attempt to fight in the air (with fly instead of hover turned on) ended quickly with me running for end (PvE wise, I don't PvP with that corruptor).
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yeah it eats end bad but at 30 my build is balanced to the extent where I can run Hide (1x end red)/Stealth (1x end red)/Entropy (2x end red)/Super Speed(1x end red) and fly (1x end red)all at the same time with no endurance degredation Stamina runs with 3x end recoveries.
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After I saw the heroes today in Sirenes, I decided to make yet ANOTHER stalker, with an even more dedicated PvP build.
The place was full of flying trollers with repel-like powers. 
(Than again, I had my 27 lvl stalker who is COMPLETELY not built for PvE ATM and is still awaiting his 32 and a respec. But the number of those trollers was almost sad.)
Ok i have just started a MA/Energy aura stalker, and finding it surprisingly fun. Although only a lowly lvl 4 i have started thinking about what power pool/travel powers to take. All i have thought of so far is recall friend, i thought it would be useful for when im sneaking around all stealthy i can then tp my team mates to me.
Are there any other pools i should pick from that might be better and/or useful?