Bethesda has focused on making great big sandbox worlds where you are free to make a lot of choices that don't matter. You can kill Bob or help Bob, but in the end all that will change is that Bob either will or won't be around later. Which doesn't matter because Bob won't have anything interesting to say if you let him live. His brother won't hunt you down for revenge if you kill him. Bob won't come to your rescue later if you help him. Bob's family won't starve if you take him out. There are a few exceptions here and there, but for the most part your choices are made in isolation and don't propagate to the rest of the world and often don't even make it to the other side of the room.
BioWare takes a different approach and seems to offer you more meaningful freedom, although once you're wise to their tricks (or you replay the game again later) you can see that a lot of your choices were illusions. They also offer a lot of different dialog choices that express different views but all ultimately lead to the same conclusion at the end of the conversation. I'm really strongly in favor of this sort of thing (a big part of roleplaying is being able to play your character) but we shouldn't confuse this sort of thing with real freedom. Like choosing how your character looks, it's a purely cosmetic choice with no in-game repercussions.
But Obsidian is taking another approach entirely, and for me it's really paying off. Unlike Fallout 3 or Oblivion, you can't choose to be a bad guy. Unlike Dragon Age and Mass Effect, you can't always say exactly what you want or noodle around in a dialog tree to your heart's content. But what the game does give you is fun and meaningful choices. These choices do propagate to the rest of the world and they do matter.
If you're used to playing a renegade type of character you might be in for a shock when mouthing off to powerful people and sucker-punching jerks comes back to haunt you later. If your playstyle leans towards the paladin end of the spectrum, then you might learn a little lesson in pragmatism when sparing the life of an enemy means they might come back to give you a wedgie in a subsequent mission. Some choices are clear, and others aren't, but after the first few decisions you'll come to appreciate being able to change the game in meaningful ways. Sometimes a choice can turn a boss fight into a conversation. Or save the life of an ally. None of the decisions follow the cheap formula of "do you want the money and the bad karma or do your want to make some trivial sacrifice as a down payment on your halo?"
Another nice touch is that they've done away with the generic good / evil slider. Instead of putting all of your actions onto some sort of universe-wide karma scale, you simply earn or lose favor with the various individuals you meet. Instead of the game passing judgement on you and calling you a jerk, it's telling you that the person you're talking to thinks you're jerk. You can't punch Bob in the face but then go and rescue ten kittens to make Bob magically your best friend. If you want Bob to like you then you have to do things Bob likes and he has to have some way of knowing about it. It's elegant, it leads to less metagaming, and it just makes sense.
Alpha Protocol is getting a bad rap for dated graphics, slow first act, and its bug collection. While it deserves to take a few lumps for buggy gameplay, I'd really hate for that to be what people remember about it. Lionhead, BioWare, and Bethesda are always selling their games on the "choices have consequences" idea, but that often ends up being more talk than anything else. But Obsidian has actually delivered on that promise and given us a game that almost demands repeated playthroughs. I'm really hoping they make an Alpha Protocol 2.
Although I hope they make a patch for Alpha Protocol 1 first.