I would either pick Clu's fight sequence from the memory road to his tank getting stuck or the lightcycle sequence.
Personally, I thought they were supposed to have GREY faces throughout the whole movie, not flesh-toned (being they are programs without blood and all). If anything, try playing with the color correction and deepen the blacks and maybe use After Effects to play with the neon lighting aspects - either enhance and make a little stronger in those scenes where it seems a little weak, or add some fine "computer etching" to the walls or some of the outfits to make them less like outfits.
All of the guards with the gas masks I would remove any shots showing the actor's faces. There are a few, but again I always thought that the face area was supposed to be all black.
Also consider playing with and adding extra sound effects - things like enhancing the bass.
For extra FX sequences, when the lightcycle scene begins, you could have an added 2 to 4 second "opener" better showing the other arenas with various battles going on -in fact, you could begin with following some recognizers as they are flying towards us, with the game grid looking as it does in the beginning screens of the TRON game. When they fly closer to us, the camera pans down, showing the flat lightcycle grid, where we spin around and head down to where the programs teleport. Extra shots like these wouldn't have to be long, but would add extra detail and depth to the TRON world say before or after certain sequences.
In the shots of the actors inside the lightcycles, I think you could add the background moving behind/around the lightcycles (I think it is just black currently), as well as give the lightcycle paths a slight glow. Hell, you could even add a 2 to 4 second shot further overhead showing how all 6 lightcycles are interacting, and do something similar to above and have the camera drop into one of the original action scenes and flow into the movie sequence.
Maybe you could create a digital "canyon" and canyon walls using IMAX blu-rays (or even some of the end sequence of 2001) to layer over the canyon Flynn flys through in his recognizer.
You could add a transparent explosion "sphere" when the MCP blows up (more like a shock wave from high speed bomb test footage than STARGATE style "rings"), do something to tweek the MCP face or even have a transparent Flynn face overlap the MCP's when Flynn jumps in (or have the eyes slowly pulse back and forth between the MCPs and Flynn's - something to show that he is trying to actually take control as opposed to just turning him blue)
Also (a BIG one), do something with the grid spiders - you could have them shooting a "web" to connect with the solar sailer path ahead of them, as the recognizers are coming from behind. You could show them scaling the energy beam ala Sylvester Stallone in CLIFFHANGER (upside down and moving fast) so at the least they aren't shown and then forgotten. Even if that is all we see of them, to actually make them part of the threat and show them DOING something would definitely justify their appearance.
Also know that TRON is coming to blu-ray I believe later this year or next summer to coinside with TRON:LEGACY. That means there will be a DVD-5 or DVD-9 sized MKV rip over at tehparadox to use as a base source for your edit.