I just got to the point where you pick three areas to specialize in, and picked Pistols, Sabotage and Martial Arts. 
For pistols, I love the ability to target from behind cover, and the auto-shot ability.  
I haven't put much into sabotage yet, but  the ability to EMP a computer instead of messing with the minigame is working out really well for me. 
And for martial arts, some of the latter cqc stuff looks really useful.
 
I'm just curious with all the "yo, stealth and assault rifle" what other specializations people have taken.

I chose to be a freelancer and a spy.  The skills I have been investing in are stealth, pistols, Technical aptitude, toughness, and martial arts.  I've also put a few points in sabotage, but I don't think I will continue on with that.

I'm rocking Stealth, Assault Rifles and Martial Arts. If I get caught I just punch people till they go down and if they're far away I kill them in a few shots.

Stealth, Shotgun, Toughness. 2 points in Sabotage for EMP-able computers and slight easier hacking. Maxed out Shotgun keeps pretty much everyone CCd, or dead in 1 blast. Shadow Operative giving 20ish seconds of invisibility allowing you to knife an entire room of dudes is also hilarious.

" I'm rocking Stealth, Assault Rifles and Martial Arts. If I get caught I just punch people till they go down and if they're far away I kill them in a few shots. "

I'm all spy all the way. I have a couple AP points in Assault Rifle, but I'm working on maxing out the stealth aspect since that seems to be the best way to play the game. 

I pretty much maxxed out Pistols, Shotguns and Sabotage and had just enough points in Stealth (5 iirc) to get the passive skill where you can see where everybody is and where they're facing.  I didn't want the skill where you could just turn invisible and clear out a room.
 
High level Chain Shot with Steel Core bullets will make short work of most of the bosses.  Room Sweep with the shotgun was kinda handy for the bosses that insist on running right up to you.  Sabotage wasn't really necessary, but hacking turrets from across the room was amusing a couple of times.

I started with Freelancer. I put most of my points into Assault Rifle, Toughness, Technical Aptitude, and Sabotage. I also put some into Pistols, Stealth, and Martial Arts.