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If you look at FFXI though all three versions are virtually identical.
Not really SE gave up and made minor UI modifications to the PC version, and the PC version is getting a major UI overhaul to modernize it sometime in the next few months.
PS2 ran at VGA resolution, 640x480, no matter what. The Xbox version ran at 720p, almost double the resolution. The PC version can now run at 1080p even without adjusting the registry, and with registry tweaks can have insane 3D background resolutions. The PC version also allows the overlay and menu resolution to now be adjusted independently, and now uses a different font set from PS2 and Xbox.
PS2 was also notorious for not allowing users to turn off weather effects like they could on PC, which was actually a big problem in zones like Beaucedine, where the snowstorms made visibility nil and slowed the game to a crawl. That's been an issue since PS2 release.
So the versions were pretty similar, but they've never been identical, and now the PC is basically going to be a different appearing game entirely.