I think it'll work out fine, especially if you balance the game with that in mind. The original annoyed me with the different EXP requirements a few times, especially Cecil and Kain in the beginning, Cecil gets his level up in a few battles, Kain takes forever.
This is something I hadn't even considered for my hack yet, I'll probably make it so that characters that join at lower levels gain levels faster until they reach the same average level the party should be at for that point in the game, then slow to the same rate as the other characters.