Here is my treatment of the sequel.
After Flynn/Clu's convergence, Sam Flynn and Quorra return to the grid and become the benevelant rulers of the grid. Think King Arthur and Guinevere.
The grid sees a period of enlightenment and prosperity (mirroring ENCOMS growth).
Meanwhile, Ed Dillinger Jr, an apple that didn't fall far from the tree, is dreaming of ways to crack the system and find glory for himself.
The brave knights, led by a Lancelot type character (you guessed it, this would be TRON!!!) have bravely fought and defeated countless attempts by Dillinger's programs(MORDRED). Piece of cake for Tron.
Suddenly, something has happened. A new piece on the board. Ed Dillinger Jr has discovered the Flynn family secret and managed to transport himself onto the grid. For the first time we have an EVIL USER on the grid. He has all the powers of the USERS. Tron is no match for him.
Dillinger's pressence on the grid creates the dark times and Sam Flynn is dying. The knights of the grid are sent out to retreive something akin to the mystical grail.
Battles between good and evil continue. Eventually Tron and the other knights find the "chalice", resurrect Sam Flynn and they go off and defeat Dillinger and the armies of MORDRED. The End.
....Pretty much a blatant rip off of Excalibur. But nothing wrong with that. The mythology is classic and tested.
IF they are committed to a trilogy, I would end the film similarly to Empire Strikes Back with MORDRED having struck a serious blow against Sam and Tron.