Kevin Flynn: It's amazing how productive doing nothing can be.
Kevin Flynn: The only way to win the game is not to play.
Kevin Flynn: Your old man's about to knock on the sky and listen to the sound.
Kevin Flynn: The Grid. A digital frontier. I tried to picture clusters of information as they moved through the computer. What did they look like? Ships, motorcycles? Were the circuits like freeways? I kept dreaming of a world I thought I'd never see. And then, one day...
7 Year Old Sam Flynn: You went in?
Kevin Flynn: That's right. I got in.
Kevin Flynn: Life has a way of moving you past wants and hopes.
Clu: I'm not your father, Sam. But, I'm very very happy to see you.
Sam Flynn: Dad?
Kevin Flynn: Sam.
Sam Flynn: Long time.
Kevin Flynn: You have no idea.
Answer: Going by Clu's behavior and personality in the film, Clu's idea of a perfect system was likely a system where every component worked as intended and as expected. One where every action by programs could be consistently predicted. The Isometric Algorithms very existence went against everything that he believed was "perfect", in that by their nature their actions could not be predicted. Users also seem to exist in contrast to Clu's beliefs as their human emotions cause them to act irrationally and erratically.
BaconIsMyBFF