Trivia: The two 'disc jockeys' in the soundbooth of the 'End of Line' club are actually Daft Punk, the French group that created the movie's soundtrack.
Trivia: In the first film, the street sign outside Flynn's Arcade indicates it's on Watseka St. In the second film, the street sign in front indicates the arcade is on Mead St. Also, the surrounding neighborhood seems to have undergone some redevelopment. This isn't really a mistake since a lot can happen in 28 years.
Trivia: After Sam hacks into the back door of ENCOM he comments: "Now that's a big door." Kevin made the same comment when he hacked into ENCOM's back door in the first movie.
Trivia: Two references to "The Black Hole", another Disney movie, can be seen in the film. There is a poster for "The Black Hole" in the bedroom of Sam Flynn in 1989 and an action figure of the Old B.O.B. robot is on his shelf next to the Tron action figures.
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.