The following is heavily loaded with opinion. Proceed at your own risk. Note: this is just a basic review.
I loved this movie (seen it twice), even though I feel like it was cut short somehow. Warblade addressed this a bit in his own blog post, but it feels like it was missing an epic ending battle of some sort. It just sort of... stopped. It had a lot of potential there, especially if Rinzler and CLU had made it to the portal platform not before, but after, they arrived, just barely, and a huge battle ensued... and that was when Rinzler had his "revert to Tron" moment.
Maybe there'll be something included in the DVD, some deleted epic scenes or something.
As for my overall impact, I did love it as I said, but I was left really grasping for why CLU was supposed to be evil. I know what they implied, they pushed a human morality onto a program, and accused him of genocide. Which is a fascinating but in the end a particularly useless thing to do. He wasn't going around arbitrarily killing like Sark in the original (after all, even the MCP found Sark to be unnecessarily ruthless and sadistic) did. I admit, looking at it from a human's perspective, it's terrible and wrong. But looking at it from CLU's perspective, you can see, or at least I can, that it's more along the lines of an antivirus that was never given full protocols as to what was and wasn't allowed to be destroyed and removed from the system. He never had what "remove the imperfections" meant explained to him, so he wouldn't know that Kevin would have not wanted him to do it. Quorra calls him "relentless" and said he hunted them all down. As a good antivirus or security program should.
There isn't anything inherently evil in what was going on. He was doing what he was directed to do, and unlike a human being, he was never taught morality. Proceed then to the fact that they pointed out several times (at least once for sure) that CLU wanted to come out into the Real World and spread here and take over. Well, conversely, what was Kevin trying to do? He had originally been trying to bring humans into The Grid and spread there. (Whether or not the humans took over would remain to be seen of course). That's where CLU got his desire to come to us, because it was one of the things foremost in Kevin's mind when he created CLU that second time.
So in the end he was more just a rival after the same thing in the other direction. He didn't need to be deleted so much as have a small amount of reprogramming. Or explaining.
Okay I'm biased, yeah, I admit it. But I'm trying to be logical as well. It's a shame about Rinzler though, I liked him as creepy as he was. (And yes I do like Tron. However if I'm going to be of the mind that CLU backed himself up, Rinzler was his best warrior and so on, he'd be stupid not to back him up too.)
I could go on, but eh, I think I made enough of my point here.