PAL: runs at 5/6 speed during gameplay. Load times are comparable to NTSC. Probably loses 7-9 minutes overall, hard to tell. NTSC-J: cutscenes can only be skipped with Start. NTSC-U: cutscenes can be skipped with Start, X or Circle.

Most people have the NTSC-U version or run it on emulator as it's the easier ROM to find. NTSC-U and J are functionally identical aside from the minor detail mentioned above. (as far as I know)