Dude! I picked those specialisations missions ago. I did every mission already, the only ones I have available to me end in an unbeatable bossfight. That's the only reason I haven't finished them. The game is essentially teasing me to restart on easy using the same build everybody else uses (stealth/pistols/cqc), defeating the concept of role playing and level progression alltogether.
This topic is in fact a gentle warning. Not many people will go with SMG's (most people prefer either a pistol or assault rifle), but those few that actually have an interest in SMG's, should know that their weapon of choice will screw them over in the end. Due to my BioWare / Obsidian / Bethesda fanboyness, I wanted to like and defend this game, as the levels itself are a blast to play. These horrid, unbeatable bossfights are slowly breeding contempt for Alpha Protocol.
Getting stuck on a boss because your build doesn't allow you to defeat him, is crap I would expect from a Final Fantasy game.