Incarnate powers are better based off of the power set than the AT in general.
Now, for stalkers the three Alphas that you usually end up seeing is Musculature, Nerve, and Agility. Musculature is the default since it does more damage, and a lot of players who don't have issues in their build simply go with it. Nerve gives accuracy and defense, and the accuracy can help out sometimes. Agility gives recharge and defense, and recharge is another way of giving more damage. The chosen way to slot these is based on what you need: If you need defense, go with Nerve or Agility. Accuracy, go with Nerve. Recharge, go with agility. If you are otherwise set, go with musculature.
Judgement consists largely of whatever you want. The ones that can be used at point blank range are Ionic, Pyronic, and Void. The ones that need to be further away are Vorpal and Cryonic. Arguably Void and Vorpal are the best for a stalker: void cuts their damage by half, and Vorpal gives you a defense boost.
Interface again whatever you need. I made another post about it which I will direct you to here: http://boards.cityofheroes.com/showp...16&postcount=7
Lore is kind of tricky, and it depends on what you want to do. If you want to just flip out and kill things, pretty much any core form will do. If you want support, different radial versions each have different buff powers that aren't listed on the wiki. Most have a heal, though. The bigger decision is whether you want to go core or radial: Radial does less damage but is up more often and has a seldomly used heal, void does more damage but is up less often.
Destiny is also about what you want to accomplish. If you are kind of a squishy stalker, you'll want barrier or rebirth. If you have endurance problems or want recharge, ageless is the way to go. Clarion is for team support or if you want protection against terror and confuse. Incandescence is for team support and leading mostly; the stun is nice but if you use it for the stun you'll tick off all the teammates who don't have a teleport prompt.
For reference, my kin/elec stalker has the following incarnate abilities:
Alpha: Musculature Core Paragon ~ damage
Judgement: Void Radial Final ~ damage + enemy damage reduction
Interface: Paralytic Radial Flawless ~ Enemy damage reduction + defense debuff
Lore: Robotic Drones Core AND Radial superior ally (I have both) ~ damage and 5% defense buff
Destiny: Rebirth Core Epiphany ~ Heal + max HP.
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/ Lambda trial guide video / Keyes trial guide video / Magisterium trial guide video / Underground trial guide
Or could go with your concept! 
Tho, as mentioned, those who have their build at the peak they want them, will tend to go Musculature for Alpha.
It doesn't really add that much to a Stalker for added defense with Nerve and Agility. So if your End Use is golden and you don't need the +RCH to obtain your best DPS, why not go for the most damage! \o/
With DB/WP Scrapper build, Musculature is what I suggested to everyone as BF-Attack Vitals was easy to obtain and maintain.
I think Void is the best to use for melee personally, but that's because it's a PBAOE. But I leave this one to concept. It's on a 2 minutes recharge anyways. So pick the one you like!
Lore is another, pick one and go. None actually fit many of my concepts, so I've started sticking with Vickies for damage and because I like the look of Vickies
Interface, solo wise, I believe the best is Reactive. But if you're not looking to just be the best solo, anyone of them with a chance for more damage is good, and going non Reactive is good if you run Trials, as lots of people have Reactive.
Destiny, as said, lots of ways to do it. Since I don't want to make my build only work in the lvl 50+ Incarnate range, I personally dont find Ageless to be that great. I get the RCH I need and ENDREC I need before then 
Though, more +RCH for heavy AOE sets could be quite nice
Generally I prefere Rebirth or Barrier, but I find them useful and concept friendly.
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Alright, completely new to the Incarnate system, but I recently acquired knowledge on using it. The thing I need help with is slotting. I originally slotted my Alpha with Agility, cause the Defense/End-regen/Recharge seemed really good, but poking around the threads, people mostly take Musculature. I'm thinking higher attack would be good, but then again, the combos at the highest Tier won't help me. As for Interface and Judgement, I was thinking of the Tohit Debuff and Pyronic, but I'm not sure.
What are the best ones for Stalkers?