One is the version 1.0 and the other is version 1.1.
Can't rightly tell you what the difference might be, since everything I dug up kept comparing the Arcade, DC, and PS1 versions of the game. Also, looking it up on Ebay and Amazon, there seems to be no form of extreme price discrepancy between the 2 games.
If you compare this to the likes of DBZ: Budokai 3 and it's Greatest Hits version (which added additional Japanese voices, special costumes for Goku, Piccolo, and Trunks, among other things) where the Greatest Hits version can go for hundreds of more dollars than the default Budokai 3, I'd say you're not missing much Soul Blade wise.
However, both versions don't utilize the same codes for stuff like Codebreaker, for some reason:
v.1.0.: Infinite Health P1: 800BFFBA 00F0
v.1.1.: Infinite Health P1: 800C017A 00F0
Figure that one out...