Can you do dispatch missions yet? I forget when that unlocks. The bottom lot of those missions reduce things like helmets.I'm around mission 10 and I'm getting a little better. I still kinda suck at going in completely stealthy and non-lethally.
Usually I can get in, but getting out is the hard part and I run off while everyone is shooting at me.
Also guards are starting to wear more helmets and gasmasks, so my preferred way of doing things is getting to be more difficult.