Alpha Protocol's four specializations become available once you've completed the Saudi Arabia operation. Depending on which specialization you choose, three skills will become "favored", allowing you to increase them to Rank 15 (as opposed to Rank 10 for "unfavored" skills). If you choose the Operative specialization, then you can manually pick the three skills you'd like this benefit to apply to. One final bonus is made available during specialization selection - you can remove any action points that you spent unwisely during the Saudi Arabia campaign.
Good spies are stuff of literature, but great spies don't let themselves become the subject of folklore. A Spy specializes in evasion and killing from the shadows.
Favored Skills: Martial Arts, Pistols, Stealth
Knowledge is power - especially when it's knowledge of explosive compounds and sophisticated electronics. An Engineer specializes in devices of high impact and low subtlety.
Favored Skills: Sabotage, Shotguns, Technical Aptitude
Few things are as dependable and solution-oriented as violence. Commandos train for situations where they're outnumbered and outgunned - specializing in automatic weapons and physical conditioning.
Favored Skills: Assault Rifles, Submachine Guns, Toughness
The dangerous and morally suspect world of espionage weeds out the rigidly minded. Most agents find their own way through life and specialize in an unorthodox variety of skills.
Favored Skills: Player-selected