I had most of the Augs by the end of the game. Didn't get cloak, useless really. If you stay in cover you can stay hidden. First you need to max your methods for exploring and getting exp. max hacking capture (you don't necessarily need the bot capture, but I got it), hacking stealth (because lvl 5's can still kick your ass even with max hack stealth, I wouldn't want to try hacking a high lvl system without it). ignore hacking fortify and hacking information these are useless.
Get the first leg aug (jumping) get super strength, get reflex enhancer for dual takedowns. Get the first eye upgrade for immunity to concussion grenades. Get dermal armor at least to lvl 3 for the emp/electricity immunity (this one is very nice because it makes you immune to electricity dmg, though it doesn't mention that in the description, you can walk in electrified water and such). Get max inventory size, get recoil redux. get max battery. I finished maxing stealth assist by the end of the game.
PS: Do these in any order so long as you max hacking and get jumping and super strength first.
Now why didn't I get smart vision? Max'd radar makes it pointless. I can see all enemies for 50 meters, and I can see what direction their facing and even their cone of vision if I have stealth enhance. No energy drain, no toggle.
Why didn't I get cloak? No need. I played through on Deus Ex, and while I did indeed reload from saves ALOT ALOT (thank goodness for that recent loadtime patch) it is not necessary to sneak well so long as you look for vents (which are often hidden behind things you need super strength to move. As for laser trips, hacking will let you get through any laser trips you can't bypass with a vent.
PPS: I got the stealth assists last.
Effectivly, just get all the passive abilities. None of the actives are really worth your time - that includes run silence. Crouching is sufficient 99.9% of the time, the only time it isn't is when there are landmines, in which case hit CAPSLOCK to walk-crouch and approach them.
PPPS: I also got Casie, because it CAN give you hidden dialogue options and in game bonuses and intel in certain convo's. No it's not necessary for the social fights- HAH, well, not until the last three anyway. Your going to fail alot without it towards the last third of the game.
PPPPS: Cloak is double useless because only your first battery cell will recharge and the game is skimpy on nutrients. So often you'll only have one cell and you'll need that for quick take downs because a non lethal takedown (or even better a non lethal double takedown) is worth ALOT of EXP. Even at max'd lvl, one battery cell ='s 7 seconds of cloak. If your stealthing right, IE being patient and watching patrol patterns and paying attention to your radar which you should have upgraded, you'll never be in a situation where you need it. Any time you face a situation where you seemingly can't sneak by an enemy it's important to remember that 1. All enemies are blind, deaf, and stupid - so long as your not immediatly infront of them. Either you CAN sneak-flank them by abusing their spitty AI, or there's an alternate path (such as a vent) to abuse. Infact, 80% of the time there's an alternate path. The other times, use cover and get behind/beside them and use a takedown a few feet away, they won't hear a thing.