The differing origin stories in Dragon Age: Origins is a decent idea, and well implemented, too bad that immediately after it becomes "now we have the set of quests that everybody gets".
The criminal or cop segment of NWN2 is a good idea but badly implemented (The thieves guild branch's storyline is just....bad...so it comes to a false choice) and then after that segment you're back to "and now the story that everybody experiences"
That was another 'ran out of time and budget' problem - the thieves branch was originally going to give you a completely different base location, to replace Crossroads Keep - If you'd sided with the thieves, you'd have been building up a place called "The Hollows" instead, and both Crossroads and the hollows were meant to be much more expansive and more detailed than it ended up being.