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It's hard to say, but my gut is that Nintendo would have a narrow victory for several years and then dominate in the tail end, much like the SNES vs. Genesis.  Make no mistake, FFVII was a huge killer app in generation 5, especially since it was released fairly early on.  It would be kind of like taking Breath of the Wild away from the Switch.  It would definitely have had an impact, but how big is hard to tell.  I tend to think a lot of Japanese CD games like Metal Gear Solid and Symphony of the Night would have ended up on the N64 too, just because it would have had that momentum from FFVII. 

On the other hand the PS1 had some other factors in its favor.  1)  It was 32 bit while the N64 was 64 bit.  That meant that the PS1 hardware would always have been cheaper than the N64 hardware.  (Although N64 software would have been comparable in price to PS1 software.)  Also, the PS1 had a fair amount of PC ports.  Tomb Raider was a PC port, for example.  GTA1 was also a PC port, but GTA didn't really help Sony until the PS2 era.  I think all of the Western/PC games would have ended up on the PS1 which would have meant the PS1 wouldn't have been lacking in games in general.  It would just be lacking the good Japanese games.

So yeah, I think the N64 would have pulled it out in the end, but it would have been close.  It would have been a repeat of SNES vs. Genesis.  A tight race with Nintendo dominating on the tail end.