I started playing Alpha Protocol last night, but haven't got very far yet. I've just finished the training section (although the achievement didn't drop, now that I think about it).
The conversation "stance" mechanic is a pretty good idea -- probably the game's best -- but a bit off-putting. The fact that each NPC builds an opinion of you, that will affect your missions1, means that every choice you're given has a chance of changing someone's mind about you, and could tip the scales against you if you pick the "wrong" one.
All of which means I end up frantically changing my mind over and over as the timer ticks down, before usually settling for the "safe" professional option. I think it's because of the way the character is presented, somewhere between the blank-canvas Wanderer in Fallout 3 and Commander Shepard in Mass Effect.
In Fallout, the only thing really governing what your character does is your own moral compass (or lack of one). There's no character background that you don't have control over, even from the moment of the character's birth. They are you, essentially, and don't have player preconceptions colouring their motives.
On the other hand, to me at least, Shepard has a back story (or several you can choose from). I've always picked the Earthborn War Hero, so I had a mental picture of who Shepard was going into the game, and the high expectations the galaxy has for the first Human Spectre meant I tended to play the noble, heroic Paragon options rather than the selfish, mean Renegade ones - because that's how I thought Shepard would act. (This is similar to how I approached Heavy Rain - I felt that the emotional connection for events came from not wanting the character to do something, but knowing that they would because that's who they were, and then making them go through with it.)
That difference could also be partially because of the switch from first- to third-person; in Mass Effect I'm not physically inhabiting the character, I'm following Shepard around and controlling him2 by remote.
In Alpha Protocol, there's just enough of a back story to stop Michael Thorton being simply my presence in the world, but not enough to weight my conversational decisions towards any of the three options. I don't know who he is, but I know he's not me - so I don't know how to act as him. I'm worried this will turn the dialogue sequences into another mini-game, trying to guess the right stance to progress to the "best" option rather than playing the story as myself (or who I thought the character should be) and seeing how it turns out.
Also, I customised him a little bit and now he looks like Wil Wheaton.
1 Apparently. I'm not far enough in to know if it actually works like that in practice, but the training section emphasised this pretty heavily.
2 Am I the only person who played a male Shepard? Everybody I know seems to have picked the female version.