Well, finally beat Alpha Protocol tonight (or this morning, at this point).  I'd played a lot of it when it first came out, then lost interest, but I bought it when Steam put it up on sale, so I finally completed it.  Here are a few thoughts:
 
1.  I cheated (used a trainer) pretty much all during the game.  Ironically, not for infinite health, but just to fully max out the skill points, give infinite cash, and infinite time for the hacking mini-game.  The RPG elements felt very weird in this game, and not super intuitive like other action rpg's (Mass Effect being a comparison)
2.  The store felt kinda busted.  I was playing on PC, and it amused me to whenever I select a new weapon to wait 4-7 seconds for the texture to pop in.  Way to go Unreal Engine 3!
3.  On that front  also, on the last mission, when you kill Darcy, chase the baddie around, etc (at least I did), the ground texture's weren't popping in right.  It took about 20 seconds of me standing there waiting for the ground to load in from a pixelated surface, to an actual ground texture.  And it's not like my computer's a huge slouch.  It's a 2.5ghz dual core, with 6gb of ram, and a Nvidia GTX 260M card.  So it's not the best, but it can certainly play most games fine.
4.  I liked some of the characters a lot, especially Heck, and Scarlet.  Wouldn't mind seeing Heck pop up in more games, just at random times.
5.  For as much as people bitch about the shooting, I didn't mind it at all.  This might've been because my character had all  the skills maxed, but I found the combat to be kind of fun.  Especially just running up on a guy and beating the shit out of him.
6.  Contrary to most other people, I really didn't enjoy the dialog stuff.  Well, I did and didn't.  I liked that it forced you to choose an option (the timer), that was fine.  I didn't like that it took FOREVER to get to an option.   Most times, I would skip the conversation so much, and then get to an option, and have no idea what they person just said.  In other games like this, written dialog shows up much quicker, and I can read fast.  Not with this game, and I was continuously out of the loop when it came to the story, because I skipped a lot of the voice acting.
7.  Nice to see Matthew Rorie's name in a game credits.
8.  I liked the radar power, that put triangles over guy's heads telling you their status.  Nice throw-back to MGS, and it's why I don't like Splinter Cell, or most other stealth games.
9.  I mainly used Pistols/Assault Rifles for my guy.  The Pistol power-up "Chain Shot" felt very over-powered.  It was a lot of fun actually.
 
It's kind of funny, because I would've given Alpha Protocol probably a 3 out of 5, like Jeff did, but for completely different reasons.  I enjoyed the combat a lot, and dug the charaacters, but I really wasn't super into the conversation trees, or the story.  I'm gonna go play it again probably, just to explore some of the other character paths, and see where it goes.