I finished Alpha Protocol last night. I think it was a pretty great game. The combat and stealth systems are a bit rough around the edges, but that's okay. It kind of reminds me of the old Syphon Filter games that way.
The thing I really liked about AP is how the dialogue choices and your actions during a mission really shape the story. Both Mass Effect games had a couple big choices in them, but AP has huge choices around nearly every corner. Pretty much everyone in the game (except the evil corporation guys, of course) are either potential allies, potential enemies, or potentially dead. It's really quite amazing.
I'm sure Mass Effect 1 & 2 kept the choices pretty simple in order to easily progress the story from one game to another, but I really hope that ME3 (which should be the end of the series, I believe.. or at least this story arc) lets you make some major decisions along the lines of AP.
Role-playing/Third-Person 3D Action RPG