The secret to this game is using the cameras most of the areas don't even require you to enter the restricted zones you just have to hop from camera to camera till you find what you need. Plus these areas sport explosive objects that can be used to thin the guards out before entering them.
The rest of the time you just need to use cover constantly. Unless the guards alert meter completely fills they will forget about you the second you get to cover. So basically you can play whack a mole pop your head up shot someone, go back in cover 2-3 secs while alert meters drain, pop back up shot some more, and then stroll through the area once everything is dead.
Usually I enter an area hack every camera I can marking all the guards and hacking all possible objects. Then I use the minimap and takes the guards out one at a time most of them are pretty split up so it's rather easy to catch them by themselves. Most of the time I just melee everyone but if your lazy you can simply pick them off with the Silenced pistol there is no need to hide the bodies either guards only inspect them once then walk off without raising the alarm
. Hell you can even use a body to bait a guard to you for an easy melee take out.
The game only gets easier and easier as you go the blackout ability and IEDs completely break the games difficulty(Last Boss I fought died in 5 seconds from 2 IEDs
) if you learn how to use them. Plus there is also Focus(Slow-motion) which I have only used 2 or 3 times because the game is easy enough without it
.
Also don't worry about killing guards there is no reward for none lethal take downs(other then some extra EXP) which really ticks me off. I spent an hour on a mission once taking out 30-40 highly clustered guards all of which had some serious fire power and took plenty of effort to take out only using melee. Thought this would avert a plot twist that I had found out about the first time I tried the mission and what do I get at completion the same cut scene showing that I brutally murdered everyone
. So basically the game doesn't care whether you put forth the effort not to kill anyone the only deaths that affect your good/evil status are civilians.
PS: On PC "T" holsters your weapon when outside of combat people freak out and start calling the police whenever they see a gun so be sure to keep it stashed in your coat at all times. On consoles I believe it is down on the directional pad from what I have heard.