People are nostalgic about the story, and in 2003 it was better than most stories in games, but they are forgetting the game is nearly 20 years old and the plotlines and story has moved on a great deal when it comes to modern games. Even Mass Effect and Dragon Age are better written because, probably because some of the same people worked on both and had matured.
I know you specifically called out the story, but also:
A lot of small environments, lots of grey or brown corridors.
Menus are really clunky, so are the controls really.
Some of the missions/quests are really obtuse and don't really give you a clear indication of where to go or what to do. That's not to say I need my hand-held, but nor do I want to be walking around aimlessly.
The turn based combat is really too easy and could certainly do with a massive overhaul IMO.