Just a few thoughts -
1. Pistol is too powerful. Armor-piercing and silencer should not be compatible.
2. Hacking shouldn't reward bonus xp.
3. AUDs for everyone, plz.
4. AI needs to be more aggressive. It should actively pursue through doors, and rooms. It's dumb as shit anyways, just make it ruthless.
5. Megan Reed
6. Non-lethal and/or THE POWER OF SPEECH options for bosses.
7. More consequences for choosing certain augs - I maxed out nearly everything, including junk I didn't need, near the end. Something as powerful as cloaking should require more investment.