So I've been playing for a couple of hours now, but I've restarted with a different approach to everything so I'm not far into the game yet. Here are my thoughts so far:
The bad
Visuals - no matter how you look at it Alpha Protocol isn't a pretty game. The character models are fairly poor (especially generic enemies) and there are a lot of low res textures and such. There are also quite a few visual glitches, especially regarding depth of field.
Bugs - there certainly are a lot of bugs present here and it seems as though the game should have gone through a lot more quality assurance before it was released, I thought that was the reason it got delayed in the first place but I guess I was wrong. I have encountered everything from grenades being stuck in the air to enemies just standing still right in front of me as if I was invisible or not even there at all.
AI - The AI isn't really all that intelligent at all. Example: At one stage I raised the alarm and climbed up a ladder to escape detection, but three gaurds spotted me and instead of shooting me like any normal (smart) bad guys would, they followed me up the ladder one-by-one. I did, however, beat the crap out of them for making such a stupid error in judgement
The good
Choices - There really are a lot of choices to make here regarding everything from who you're gonna befriend or piss off to what weapons and gadgets you're gonna take with you on missions. This certainly isn't the watered down roleplaying you'll find in other titles such as Mass Effect 2. There is a shitload of customisation, I have been stuck in menus for ages trying to decide what to buy and what skills to upgrade, etc.
Story and dialogue - The story and dialogue are brilliant, as is the norm when it comes to Obsidian games. I really like the dialogue system and how the game forces you to make quick decisions during conversions that will have on impact on the game's story and how characters perceive you and treat you. I haven't played long enough to see how my decisions and attitude towards certain characters will affect things in the long run, but I have discovered optional side quests as well as bonus ("secret") perks by just playing around with the different stances during conversations.
Overall
I really haven't played enough of the game to give a fair opinion about the grand scale of everything, but so far it looks like the good definitely outweighs the bad. I'm really enjoying the story and found it quit surprising how funny some of the dialogue is. This game looks like it was made with people like me in mind, people who don't care about bugs or "poor" graphics, people who like to really spend time with roleplaying. As I've mentioned there is a lot of customisation and you will most probably spend a lot of time reading intel, deciding which skills to upgrade or which weapon or armour upgrades to buy, etc. Obsidion have clearly dedicated most of their time with this game on creating a rich and deep RPG experience. Unfortunately other elements of the game such as the visuals and AI seem to have suffered from it and this will result in a lot of people hating the game for it and never playing past the first few hours.
Will try to give a more in-depth and final opinion once I have played furuther into the game or once I have finished it once and seen just how big an impact my decisions have made on the story and how characters treat me. Things are looking good so far as I'm really enjoying all the decisions as well as the story so far.