Just posting a poll with this for the sake of curiousity. (I voted in favour of the SegaCD version because I've seen what they did to it for the PSX version)
I'm playing through the original SegaCD version right now, and I'm utterly blown away by how rich the story is. I'm really beginning to think the fact that it was the best selling game of all-time for the SegaCD, is an insult to the game because of how quickly the console died. I've only just made it to the Nanza Barrier, and I am getting the feeling that the game is only going to keep getting better. Not to mention the soundtrack is EPIC! Especially the 'new' overworld music, it kind of reminds me of the theme from FFIV
My only problem with the game is I'm STILL trying to figure out the mechanics to changing the party's order rather than just selecting random people until it's in the order I want.
If you've never played this game, and you like the Final Fantasy franchise, I IMPLORE you to play it!