Well, for one thing, FF would not have ridden the wave of popularity that 3D gaming brought in the late 90s, meaning the series and perhaps even JRPGs themselves would have stayed a niche genre. Square would not have become super popular, and several side projects probably would have never left Japan like Xenogears or Dew Prism. The Spirits Within would not have been financed and thus Sakaguchi would most likely still be in charge of the franchise. We may not have ever seen the MMO entries as well. KH would probably not exist.

To tell the truth, I can't really fathom the franchise not going to 3D eventually. Unlike Dragon Quest, FF has always been a bit more flexible with its fanbase about changes.