Yori or Ma3a (I'd be happy with either one, as I've even told Cindy Morgan, though I told her that I'd prefer to see Yori again a lot more).
Tron 2.0 isn't considered canon in the movies. Which is unfortunate.
True,
TRON 2.0 isn't canon, but it could still be used as a potential source for ideas. For example, since Sam Flynn may be doing more experiments with the Shiva Laser, he's going to need a program that can handle the new lab and laser. Since Yori may not be able to run on modern computer systems the way she was designed, there's a good chance that she could be upgraded to become Ma3a so to function on more modern computers (changing the background information on Ma3a would have to be done, since Lora Bradley was seen alive in well at the San Francisco event for
Flynn Lives). Or Ma3a and Yori could both be involved, both being two halfs of what is required for the new lab to function properly (with Yori handling the laser's primary functions and Ma3a handling the correction algorithms needed to make sure that a user comes back out in the same condition they were in when they went in. Let's face it, we don't want to see a repeat of the Baboon incident from Cronenberg's
The Fly, do we?). Me, I'd prefer to have just Yori back, but have her be upgraded from the program she once was to being responsible for the correction algorithms that Ma3a handled in the game.
In fact, with what's hinted at in
The Next Day, Dillenger Systems seem to be planning a hostile takeover of Encom from inside and out (sort of in a similar fashion to what fCon does in the game). So, why not recycle the game's story (which was originally meant to be used for a film sequel for
TRON anyway) for the next film? Just revise it, make sure it doesn't conflict with the film's canon and viola! Besides, I'd like to see a film version of Jet (who could be the Han Solo to Sam's Luke Skywalker).