So, when Legacy came out, Disney all but said it was non-canon. To which I say "FEH!" It is my opinion that 2.0, which has a rich story for a videogame and limited 6 issue comic run, can fit perfectly into the established Legacy canon, with the changing of a few minor details, and assuming something happened that was set up earlier.
*WARNING*THIS CONTAINS SPOILERS!*WARNING*
First things first: We must assume that Flynn figured out the digitizing algorithms much earlier than they did in 2.0. Either that, or Alan and the team figured them out earlier. It has to be solved one way or the other before 1989.
Number Two: Flynn leaves the company in '88 or '89, just before he disappears into his private Grid system. Easy, right? The game had him leaving in 1990. Link
for proof. The only other mention of Flynn is an email in 99 when he asks how Alan's holding up. Easy to fix that one, just say that second email never happened. Kevin was too busy trapped in the Grid.
Number Three: Lora has her digitizing accident, and is partially or completely integrated in the the Math Assistant Audio series (Ma1a, Ma2a, Ma3a). However, the experiments conducted with the backup Jet in Ghost in the Machine provide options to get her out of the system and back into the real world. And then she's back in plenty of time for the press conference that Sam dropped in on in the Flynn Lives ARG.
Anything that doesn't fit that I missed? Any thoughts on how it could work better?