I still haven't beaten this yet. I have like 2 more endings to get. The Ark is just so frustrating....it's everything I hate about Knuckles' Adventure levels rolled up into one area...motion sickness included after 45 minutes.
If they want people to forget it happened, why are both Crisis City and Silver the Hedgehog in Sonic Generations? Generally speaking though, it does seem like they want to forget it happened. Still, it would be kinda fun to see what hackers can do if it ever gets released on the PC; their scrapped idea of playing as any character in any stage springs to mind.