Choose augmentations based on your play style, and get the ones that will benefit you the most.

Cranium: Capture is the most important, as you must be able to hack successfully. Do not waste points on Social Enhancer, Hacking Stealth, or Fortify.

Skin: Invest in the cloaking upgrade to keep your character invisible as long as possible.

Arms: Heavy Lifting will help open doors and move crates.

Torso: A faster recharge lets you use your special skills more often.

Eyes: Upgrade the radar and get the augmentation to see through walls if you have the points.

Legs: Being able to run silently is very useful, especially when you have enough energy to combine it with cloaking.