Alpha Protocol was "officially delayed" to the amorphous "Spring 2010," but, unfortunately, that didn't happen. Speaking with MTV Multiplayer this week, though, assistant producer at Sega Matthew Hickman explicitly detailed the reasons for the delay, saying, "We really wanted to polish the game up, make it everything Obsidian planned it to be, and give the consumer a very polished game."
He added that there's been some "tweaks in lighting here and there," and the inventory screen has been revamped a bit, but in general the team has been focused on "bringing the whole quality level up." The post's author also notes that the game is set for a "Summer 2010" release window now, and we've reached out to him (and Sega) for clarification.
Update: The post's author has responded that, yes, the game's current release window is set for "Summer 2010." Guess that's another delay then, eh? We'll update again if Sega responds.