Yeah, that script did look like it was the result of some serious chaos in the writing process, different writers with incompatible ideas about what the story should be. Do you know what the original plotline was?The original script "Tron 2.0" was completely different from the story that we saw on the screen.
Another Con is that CLU's mania for perfection didn't synch with the very imperfect and human way that he and his programs behaved. There was nothing remotely "perfect" about any of them, it was basically just human society re-created, complete with bloodsports, sleazy clubs and palace intrigue.
Which I liked, btw - the idea that AIs are creating this zany world on their own is fun and a lot more interesting that if they'd been Borg-like automotons of perfection.
But if CLU has no, well, clue about what he's doing, it undermines his credibility as a villain and just renders him pathetic. A good villain needs to be smart and powerful so he's more of a threat to the hero. His point of view may be bad but it needs to be accurate and internally consistent.