1) The first perk you should go with is Regeneration Overflow, so when you stop shooting to regcharge your shield (the blue bar), the first hit you receive won't damage you.

2) The next most importante perk is Extra Plating. Make sure to get all 3 levels of it, cause it's a huge armor boost.

3) Third most important perk Jack of All Trades, it will increase damage for ALL of your weapons. It might not be available right away, but get it as soon as you see it.

4) Follow with Plasma Expertise. I took this one to level 2 to make up for Wave Blaster / Pulse Cannon's lower damage compared to machine guns.

5) The other two perks I chose before finishing the game: Quick Loader (faster fire rate for bullets) and Conservation of Energy (it'll add energy to your shield when you kill something with a Plasma weapon).