I kind of understand that the writers on the sequel don't want to be shackled by the stories that came before. But as long as previous story ideas don't conflict adversely with what you want to write: why not at least try to make what you're writing, fit with previous continuity?
Now, we haven't seen the film yet. So we can't honestly state with certainty how much of the film's story conflicts with Tron 2.0.
But at least one thing seems clear at this point. The film is ignoring the fact that digitization technology was lost for at least a decade, and Alan rediscovered it through Ma3a. According to what we've seen from the film, Flynn digitized himself back into the computer only a few years later.
It would have been simple to reconcile the film with the game's story. Just delay Flynn returning into the computer world for a few years. Then the whole "Alan rediscovers digitization" storyline could have been left intact. But no, they had to go and abandon that. I thought the whole story of what Alan (and Jet) had done in the meantime during all these years, was a good one.
It could also explain why Flynn didn't immediately go back into the computer . . . it's because he couldn't.
As much as everyone sneers at George Lucas these days, I'll give him one thing. He's tried his best to keep the Star Wars expanded universe and continuity from becoming a mess. He has people constantly checking new stories against existing continuity, to try and make sure everything falls in place. (Of course, then Lucas had to go and retroactively mess with his own continuity in the prequels.
And even though I'm pretty sure Lurkinghorror also wasn't too happy about being burdened with making his story fit with an earlier one: I appreciated the fact that the Tron comic respected the established continuity of Tron 2.0.
I wish Disney would take more care with the Tron universe than they currently seem to. But who knows, maybe that's slowly going to change.
P.S. Again, I don't know why this isn't posted in the Tron 2.0 section?