I agree with Cep. While the game gives you 3 specializations, in actual practice I find that because of the amount of AP you get per level, it's more realistic to just decide on 2 main skills to keep maxed out at any given time.
Whenever you have AP to spare, you can throw them into whatever you feel would benefit you most at that point of the game. It could be that you find that you could do with a bit more health, or maybe some support on gadgets or hacking, or better handling of another weapon, or some boost in CQC abilities. Whatever suits the situation.
Because of the way the game is designed, you generally want to ask yourself a single question for a character build:
Do you want to play a stealthy character of a guns blazing character?
Stealthy character = Primary: Stealth.
Guns blazing = Primary: SMG or AR.
This, imo, is the backbone of most character creation for the majority of players. Once you have this primary skill in mind, the next decision will be whether you want a pistol specialization. It will benefit both play styles, but it will benefit stealth play style much more. Those who are playing stealth and do not want to focus on a pistol should then put all the other points into CQC. I would advice against specializing in stealth alone and then picking another non-combat skill to train extensively in, because at some point you need weapon skills. Since most stealth players will want to try to make as little noise as possible and not kill if needed, the pistol is the only real choice.
For action hero characters, as long as you have specialization in a heavy weapon, you can pretty much kill all the bad guys easily. It would hence be best to place points into things which help in other ways, instead of putting it into another weapon which you probably don't really need. Sabotage is good for making your life easier when you need to remove alerts which you will definitely be setting off, as well as making clearing mission objectives which don't involve shooting the shit out of people much easier. Alternatively, if you feel you need more healing and stuff, Tech is also a good skill to have.
Players who want a lot more variety can obviously try many other types of builds, but I think this covers the basics of it. For an average playthrough in the game, there will be enough exp to max out 2 of the 3 specializations you make, there should generally be enough to max out all 3, but not always. This is why it is best to mentally pick 2 main specializations, and spread the rest out as you see fit.