Developer Obsidian has become known for flawed (or even ruined) masterpieces, and Alpha Protocol follows that tradition. Fortunately, the game is more masterpiece than flaws, but the flaws are still there. If you want the full list you can check with Yahtzee and Susan, who both reviewed the game. But I hope other developers take notice of this one, because Obsidian is doing something that should be shaking up the RPG genre.
People who are into tabletop rolepaying games will point out that pen-and-paper games offer freedom that computer-driven games can't match. This is true, but I think sometimes the "total freedom" thing is both oversold and overrated. Even tabletop games don't have total freedom. If one of my players decided their character was going to retire from adventuring and open up a unicycle repair shop, then I don't think I'd want to keep running a week-to-week simulation of their shop and roleplay a bunch of unicycle customers for them. And I don't think the other players would want stop their epic adventure while I ran the game for the unicycle repairing character while they swept up their shop each night. If you're playing a tabletop game, you have to come to terms with the fact that you need to be on the same page as everyone else in terms of what makes the game fun. This is often a lot more restrictive than it seems. The point is that we don't really need limitless choices in a game in order to have fun. What we need are choices that are interesting and fun.
Videogames are usually about making choices. There are a few reflex-driven games where the gameplay boils down to doing things exactly right or failing, but for the vast majority of games players have some kind of freedom to decide how they will face challenges. In some games the choice is something primitive like, "Do I shoot this dude with my shotgun or my pistol?" That may seem like a trivial choice, but imagine playing a game where your character would move from room to room and there was never more than one door to walk through, one chest-high wall to stand behind, and one weapon to use on the bad guys. I don't care what the graphics are like, that game is going to get old in a matter of minutes. Even for non-roleplayers, choice and freedom (or the illusion of them) are an important part of what makes the game fun and what makes the world engaging.
This freedom takes center stage in an RPG. Or it used to. I've said before that we don't quite have the freedom we used to in videogames. The skyrocketing costs of graphics and voice acting have put the pressure on the other areas of the game, and freedom of choice is an easy place for a developer to make cuts. Different game designers have handled this in different ways.
(I know the term "RPG" is an absolute mess, almost to the point of having no meaning at all. For the record, when I say "RPG" I'm talking about games from the likes of BioWare, Obsidian, and Bethesda and not Square Enix, Blizzard, or Lionhead. Someday I'd love to have terms that clearly differentiate between "leveling up" and "roleplaying". But today is not that day.)