Because - and I realise a lot of people are going to object to this when I say it - the games are trying to tell you a story. Video games are a valid and indeed a brilliant medium for storytelling. Just because they (and RPGs in particular) allow you a drastic degree of control over what goes on in the story doesn't mean that the story can't - or even shouldn't - be pre-written to some degree.
This is why, for example, Shepard can't join the Reapers. It isn't a story about some space-dwelling fellow who joins the evil invaders, it's a story about a heroic man who goes to war with evil invaders in an attempt to save the universe. You might get to decide what kind of hero he is, how he goes about his attempts to save the universe and even whether he is ultimately successful, but the story is the story. You decide how it is told, you don't get to rewrite the entire plot.
Lastly, it's just not feasible. A game with a huge sprawling world about a guy fighting against a big bad is so much different than a game in which you're working for the big bad. All the missions, dialogue and stuff have to be entirely different. It means making two games (albeit with mostly the same assets) when most players are only going to see one of said games.
Plus, it basically begs replays to see both potential tales, but the idea of signing up for the enemy's team when you meet him could make that kind of a chore. You're going to have to replay everything else up 'till that point. And it's not like you can just spring the choice on your character near the beginning of the game. If they don't know the game's lore, information on the enemy and his motivations and goals, if they haven't had a chance to hear out the opposite side, to see and get to know the world and the people that will be affected by the choice, how are they supposed to make a meaningful decision? So you're going to have to slog through about half the game again. And it's not like you can have (m)any meaningful decisions before that point either, since a big change-up like joining the villain half-way through the game is going to change everything thereafter.
It just isn't really doable on both a technical level and from the perspective of the storyteller.
