1. It is boring and clichéd even though it obviously attempts to not be
Quorra doesn't sleep with Sam and they all talk like it's a cheesy 80s movie, and not in a nostalgic cool kinda way, man.
2. The plot makes no sense
Clu is an asshole and totally throws off Flynn's Zen, why is he such a buzzkill, dudebro?
In the middle of the movie when Sam meets Kevin Flynn at his hideout he explains what happened to the Grid:
That he created the program Clu (an apparent clone of himself) to create "the perfect world". Then he talks all about the ISO's. But this is where it gets tricky:
Flynn then explains that Clu staged a coup of the Grid and attacks Flynn and Tron.
But why? Why would a program decide to take over and turn against its creator? This part of the story seems to be the most important, and yet it only gets a line or maybe two. They really should have given this aspect of the story more depth and elaboration.
"What about the ISO's?" you might ask.