Atari + Amiga would have taken a different development path, but still been call a "game system", and eventually would have faded just as with Commodore. The only way I see anything could have survived long term is if Atari/Commodore merged resources and made a serious attempt at next gen systems with a more open architecture for a wider market that could have kept it going through the rougher times kind of like Apple. Heck drag Palm in to the mix for the PDA device market too. 3M didn't know what to do with it. In that configuration MAYBE it would have been different today. As it was, neither Atari or Commodore had moxie enough to survive the desktop wars.
Plaz