Spoilers ahoy!
How I would fix Tron Legacy:
1. Shorten the introduction. By the end of the first reel of the original Tron (a reel is between 15-20 minutes, normally. Shut up, I'm a projectionist), Flynn is in the Grid. It takes Sam roughly twice as long.
2. Ditch the CLU wants to take over the real world plot . That is preposterous beyond my capacity for willing suspension of disbelief. Instead, make it about, say, CLU wants to take over the internet. You can even keep the whole CLU wants to create the perfect system plot with it. You can't tell me that he wouldn't consider the internet to be a deeply flawed system. He also needs Flynn's disc to fire up the 14.4k analog modem/portal. .
3. Thus, the ISOs came from the internet. You can even have a 4chan ISO, but I'd probably advise against that.
4. Come to think of it, give the ISOs a new name. I've dealt with my fair share of disc images and they haven't revolutionized my life in any appreciable fashion. Also, none of them look like Olivia Wilde.
5. Let Sam act like he's enjoying himself every now and then. Consider Flynn in the first Tron. Even though his life is in danger, he always seems to be having the time of his life. Who's obviously having a good time in Legacy, other than Castor/Zuse, the traitorous slimebucket? Nobody, that's who.
6. Make Flynn and Sam's reunion less awkward and boring. Maybe it should come later in the movie? Make Sam actually work to get there? I don't know. The thing is, it wasn't as awesome or emotionally real as it should have been.
7. Explain why Flynn needs to "reabsorb" CLU or at least give him a sacrificial death that makes sense .
8. Bits. Maybe even some bytes.