I'm one of those guys whose first Lunar was the PS1 version, & I love it to pieces compared to the Sega CD version, I'll assume it has more to do with what's been changed, rather then what is or isn't better perse.
I prefer the Saturn Lunar SSS' and the Sega/Mega-CD Lunar EB. To me, the combined games make up the overall story/experience. I didn't like the GBA Lunar though and haven't tried any new Lunars since.
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I used to have the GBA Lunar & couldn't stand it, so I sold it. I have the PSP Lunar, it's decent, though, I still prefer the PS1 version.
As for what Nod said about the adjusting of bosses in the PS1 game, that is deffinitly one thing I've never liked, so I deffinitly agree on that!