This game doesn’t really need an aug “build guide” the way Deus Ex did, since you don’t have either / or choices. You don’t get enough experience to buy everything, but you aren’t locked out of choices either.
That said, here are my opinions:
Rank 1:
Hacking / Capture, Hacking / Stealth. There are door locks everywhere, and you get a constant stream of XP and money from hacked devices. To the point it usually makes sense not to use passwords you’ve found. The big drawback is getting this maxed out costs a lot of points.
Arm upgrade: move heavy objects. It’s cheap, and the designers like to block things with heavy stuff.
Cloaking. The cloak is sort of the all-purpose solution to most situations, and it takes the risk out of timing guards.
Eye upgrade: look through walls. While the radar often picks up on hostiles before you see them, being able to look through closed doors prevents all sorts of nasty surprises.
Rank 2:
Arm upgrade: smash through walls. Cheap, and there are lots of places to use it, often with stuff behind them. The drawback is it’s loud, it alerts everyone nearby. Breakable walls aren’t nearly as common as locked doors, though they often give you a way past locked doors if you didn’t take hacking. Would be rank 3, but it’s only 1 point, unlike the other path-openers.
Social mod. Gives you “pheromone power” in many conversations, though not really that helpful for “boss” conversations. 2 points, but talking your way past people saves a lot of headaches, so it’s a bigger deal than other path-openers like wall smashing and jumping.
Rank 3:
Carrying capacity. You don’t really need more space, since you can get a lot done with compact weapons like pistols and the stun gun, but it’s tempting to pick everything up you can find.
Leg upgrade, jump higher. This opens up alternate paths, but not as many as hacking or smashing through walls.
Reflex booster: take down 2 opponents. This would rank higher if it weren’t so rare to find two guys close enough to use it, or if it worked when one or both targets are sitting. Still, it lets you surprise two targets without raising an alarm, and that’s a big deal.
Eye upgrade: flash immunity. True, the enemy almost never throws flash grenades at you, but this renders you immune to your own concussion grenades, so you can use them at close range like Ninja smoke bombs.
Rebreather. Opens up some paths blocked by toxic gas, but more useful for immunity to your own gas grenades and mines.
Hack / Turret, Hack / Robot. Very situational, but being able to turn off turrets is a big deal. Biggest drawback is that if you use them to kill your enemies, I think you lose the Ghost and Smooth Operator XP rewards. Not sure about that, though.
Typhoon: I didn’t use it much for regular enemies, but it makes short work of bosses. Highly situational, but very powerful when you use it. Lets you kill a lot of enemies without losing surprise.
Energy upgrades. Obviously candy bars solve all energy problems, but more bars means you’re under less pressure to eat more candy while doing something else, and faster regen means you have fewer situations where you have to gobble a bar in a hurry.
Rank 4:
Dermal armor. Doesn’t really reduce damage that much until you get to rank 3, and generally speaking, you can get a lot accomplished without anyone shooting at you. A fully-upgraded cloak is even better protection if you do get in a firefight, with the drawback of using energy.
EMP shielding. Expensive to get to, but does open a few paths where the floor is electrified. Those aren’t that common, though.
Fall silently. There are lots of places this is useful, but it hideously expensive to reach. Would be rank 3 if it weren’t 3 points on top of Jump.
Rank 5:
Stealth enhancer: kind of useless, except that it upgrades to Cone of vision. For 3 points total, you get some fine detail on who can see what on the radar. Marginal because the basic radar tells you almost as much.
Icarus Landing System. It looks cool, and there are one or two places it lets you bypass stuff, but usually there are alternatives already opened by the other augs. Mostly seems like a convenience.
Aim stabilization. Fixes reticule sway when sniping, but usually you get get hits at long range without it.
Recoil reduction. Doesn’t affect a lot of important weapons, and you can go a long way without it. In fact, I never took any.
Neigh-useless:
Radar upgrade. Great on paper, awful in practice because it makes it hard to see who is facing where.
Mark-and-track. You can already see this on your radar.
Alarm countdown. Knowing how long you need to wait makes no real difference.
Hack / Analyze. Completely useless.
Hack / Fortify. Not completely useless, but Hack / Capture and Hack / Stealth do everything you need.
Run faster, more sprint time: almost never felt any need at all for more speed.
Run / sprint silently: I’ve never alerted anyone by running.
