For game systems, SNES was on 65816, Sega Genesis was on 68000, and I don't think it really made that much difference. Both systems had exactly the same games, sometimes, obviously built with the same art, probably from the same source code to both platforms. SNES was a hint, that chip was available cheap in large quantities, but yeah, I don't think Antic/GTIA was on the path to evolving to take on something like Sega Genesis.
On the PC side, pre-VGA, games were getting built from C rather than assembly, so anything with 16-color, 320x200, probably might have gotten a conversion if there were enough units out there. It would have fit more in the Tandy 1000 category, I suppose. An upgraded 8-bit with ST-level graphics would have obliterated ST completely, kind of my take. That basic the same games, but people can still plugin their old floppy drives. Would have been a natural upgrade path to all those XEGS buyers, and old 8-bit people. Atari would have hobbled together a GUI of some point, but GEM wasn't that great either. The problem is that it'd have taken slightly longer to design, and that delay might have been a deal killer.
On the applications side, Atari was just doomed because of Gem, is my take. The UI was sloppy, the rules for programming a compatible game that would survive upgrades were unclear. They had 68000 just like Mac but they never made the jump to the next CPU, not really. When Atari went to 68030 too much stuff broke and those platforms all failed pretty hard. Tramiels never cared much about backwards compatibility, but by the late 80's and 90's, it mattered. I don't think they got that, and that's why they failed.