I'm okay with this, actually. It took them 20 years to figure out a storyline and presentation that even remotely worked. I don't know how the hell they were going to explain Quorra in the real world, or any of the ISO stuff for that matter...they backed themselves into an unsolveable situation with that whole part of the storyline in terms of continuance.
I think they can wait a few more years, come up with a better storyline, and do it. Personally, I'm a big fan of the Tron 2.0 game that Monolith released way back, where you had things like viruses and corrupted programs. Legacy didn't take anything like that into account, because they were still on the same isolated system inside the computer world. I think that part HAS to go for the franchise to have a successful third movie at this point...it can't be limited to one mainframe, it's got to involve a bigger world. That's kind of where I feel like Legacy failed. I still love the movie, but the time right now isn't right for a sequel and I'm glad to see they canned something that was seeming like it might be half-assed.