Firstly, the finale file locks you out of an entire zone, the world where the finale itself takes place. This is bad if you're trying to unlock the true ending on Normal because you need 100% completion. The game doesn't warn you it's going to be doing this stunt (and certainly not of its flaws), so you have no choice but to go back to your old file, clear it and create a new fourth file, overwriting any progress you may have foolishly made in the old, nevermind that that's a complete rigmarole. Furthermore, progress in the fourth file just sort of lingers separately, leaving you two near-clones of the same character for multiplayer purposes, which is an even bigger deal in the Japanese expanded release as it has extra sections in the fourth file! (Unless the expanded release creates a fifth file, yeesh. I wouldn't know.)
There are hints throughout the game that there was originally only going to be one file and they changed gears, but this was not the right gear to change.