You miss my point. Stripped to their basics, the plotlines of any story are going to have been done many times before. The issue is how unique and interesting the execution is.
In that sense, most RPGs don't ever break beyond the 'bad guy wants to do bad things' barrier; Sarevok wants to slaughter lots and lots of people so he can become a God. Irenicus wants to slaughter everybody in his old homeland for preventing him from becoming a God, and also to give becoming a God another try. Mellissan wants to kill all the Bhaalspawn so she can become a God (notice a trend?)
I wish I could tell you what the villains in NWN wanted, but I got bored around Chapter 3 and quit playing. Something about ancient lizard people conquering the world. I wouldn't be surprised if some villain or another was planning to use the slaughter of everyone in Neverwinter to become a God. Or something.
The Fallouts are the only ones which comes close to breaking the barrier....but even there, with objectives you can kinda sorta see how someone might believe in, the objective is pointlessly genocidal and obviously 'bad.'
Of them all, the only one which transcends the tired cliche is Torment. You can point to the amnesiac thing all you like, but beyond the set-up virtually everything in Torment is outside of your typical fare....and executed brilliantly, I might add.