I've read some of the negative reviews, particularly Destructoid's and it sounds like the criticism is way overblown. It seems like they're complaining about the hacking/lockupicking mini games actually being a challenge. God forbid we have a game where hacking mini games aren't a tedious bore with no challenge whatsoever(sorry Mass Effect 2, you're one of my favorite games but you're still guilty of this.)
Also, I think the AI is much ado about nothing. Yes, it's not the best AI we've ever seen but it's functional enough for stealth game. Deus Ex had pretty lousy AI but that didn't stop it from being a great game.
Also, the game is pretty polished overall. There are a few glitches but not nearly as bad as I was expecting based on what I've read in the reviews. The only bug I have encountered in fact is one where the game freezes when it loads a check point after you die but it happens very rarely.
Alpha Protocol is a great game and I'm pleased some reviewers like 1up realize this.