You say you have a dark/regen scrapper at lvl 50. Maybe one of the new dark/* stalkers would suit you.
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Personally i like the SR pool as a secondary. my Stalker is slotted up as far as he can go on the defensive side of things and he's one tough cookie in PvE. only 2 down sides to SR (as far as i can see) is that when you get hit you take the full force of the attack and there is no-self heal in it, carry Greens and you should be ok though.
I have Claws as a primary which is also a cracking pool dispite Leathal damage being widely resisted, esspecially at higher levels. Claws has a fast recharge of the powers plus 'Quickness' (+recharge, +spd, resist Slow) from the SR pool really helps matters.
I feel these two power pools compliment eachother nicely
I played a claws stalker to level 32 and was completely underwhelmed by the high level attacks. Don't get me wrong, they're useful, but just not particularly uber. They are AoE's which is nice, but not particularly big ones and they don't do much damage. On a DPS measurement they might be quite good, but claws will have improved DPS soon anyway, what you need is a nice big finishing move after AS.
With the new animation times being reduced for the lower level powers, there's even less reason to take the last two attacks. However, Focus is a fantastic power, the set's jewel imo. Good damage, good knockdown, good recharge rate, available fairly early and its ranged on top! Good for the stalker that wants to stay out of the mass melee.
Anyhow, I ditched my level 32 claws/nin for an Energy Melee/Super Reflexes. On the whole, I prefer EM and I'm looking forward to the two big high level attacks, great follow ups to an AS. The AS power looks super cool on a claws stalker but isn't as good looking on an EM. However, I love Flight and so have Air Superiority in my attack chain, which I feel is needed at low levels unless you don't mind hit and run tactics all the time. Air Sup doesn't really work with Claws as it forces you to put them away and then redraw them, very annoying. But then Claws doesn't need any extra attacks, the ones it has do fine damage and recharge fast.
I also think Ninjutsu possibly has the edge over Super Reflexes. It was designed for a stalker and has some useful powers, but SR is all about defence... unfortunately it takes nearly all the powers to get it and you do have to take Stamina to run all those toggles.
SR lacks a heal and for the life of me I can't seem to fit in the Medicine Pool for Heal Self. I think this might be a problem at later levels, we'll see.
Finally, I've no room for any epic powers, SR really eats your slots unless you're prepared to have Ninjutsu level defence with no tricks.
My advice :
Claws for scrapping PvE, EM for a proper stalker 
Ninjutsu for tricks and cool stuff, SR for hardcore no nonsense defence 
My two inf.
What do people think to Dark/Energy Aura since we're on the subject. I like the idea of a -acc effect primary with a defense based secondary but is Energy Aura any good?
Energy Aura is probably the weakest stalker secondary in terms of defence but given the usual Stalker playstyle, that shouldn't matter, unless you're going to stand and scrap. EA's real problem is a lack of a heal, so see if you can fit Aid Self into your build. Otherwise it's quite good, with low-cost toggles which can be taken early and two end powers which aid non-stop stalking quite well.
"I know 653 ways to kill a man. Fist to the face is #56."
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What do people think to Dark/Energy Aura since we're on the subject. I like the idea of a -acc effect primary with a defense based secondary but is Energy Aura any good?
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The -Acc effect on DM isn't that high, think it's only around 1% even with 3 slots? Not sure though, that's what I remember being told. Doesn't make much of a difference on my LvL 50 DM/SR anyway.
But, for a Stalker, go EM/Nin. Amazing combo, I've recently rolled one after getting a Nin/Nin to 40, and I've fallen in love with my EM/Nin! It has both the def, and the heal, which work quite nicely together. There's the AoE Placate too, but it's quite frankly not too great. Definately go EM/Nin though. If you want an example of how effective this combo is, go to Thatslyfe.com and check out Elernet's PvP videos in the Media section. Pretty amazing stuff.
The -Acc is 7% up to 15% with 3 slots, and ToF has 25% with 40% at 3 slots.
And thanks for all the ideas guys, I really appreciate the consensus.
Now that Issue 7 is soon to be hitting our doorsteps, I'm probably going to ewnd up creating a Stalker to have a change from my MM every once in a while.
Now, I have a Dark/Regen Scrapper as my main lvl 50 at current, but I cannot seem to find any Stalkers that suit me. I've tried Nin/Nin and Claws/En highest (lvl 20ish), although I've looked at quite a few different combinations.
I quite like the Energy shields because you get all your necessary shields before you get your travel power.
I've noticed Brutes also work like that with their exclusive shields, although I won't get into that, even though I may create one also.
OK, so I basically need help with choosing my powersets, as I can't find anything to suit me. Can anyone help?