You know, I gave it some thought and, while I have lot of issues with Alpha Protocol (I dislike the type of story it tells, the various interactive systems like sneaking, hacking and combat aren't very good, etc), there is just one thing that really kills the game for me. It is the way the game handles choice. In most RPGs, you are given at least some semblance of initiative, free will or control. In Fallout, for example, you can go wherever you want on the map, you have dialog options to express the most basic options and what happens to each town after the game ends is foreseeable and controllable. You don't have just "choice", you have initiative, you have enterprise.
In AP, on the other hand, the game tries to give you a few choices, each of which will change the story in wildly different ways. Throughout, it even robs the player from having a good idea of what his choices will do. Besides the "stance based" dialog, where you can't even know for sure what you are choosing to say or do, the game can also dictate what your character does in certain situations. To be frank, I am still pissed off that when I stealthily approached the guy you need to take out before the tank boss battle in Saudi Arabia, the game suddenly went into cinematic mode and prevented me from doing what I wanted to do.
I think I understand why they did it. By having the choices limited and having their consequences as a direct part of the story, the game can make Thorton and actual part of the story, not just an spectator. To expand on what I mean here, take Vampire: Bloodlines as an example. You actually get a few choices in that game, but even so, most of the time, the story you saw in that game was mostly about other characters. And while I think AP's is a very noble goal, it made Thorton not actually seem the player's character, but someone else's. Torment, for example, frequently managed to make TNO part of the story being told without taking the player's control (although I admit Torment wasn't anywhere as successful here as AP).
In a way, I think the game is closer to those japanese visual novel software, where one little choice can send you in a wildly different story, though I do admit AP isn't anywhere near that bad for the most part. I understand a lot of people here liked AP and while that is great (heck, I wished I could enjoy modern games like people here seem to do), but I really think that player initiative, or enterprise, is a crucial thing for an rpg (or at least my definition of rpgs).
Anyway, thank you, SCO, for a good read.