The problem with that kind of customization is that it makes the characters less unique. In VII and VIII you could basically use any character anyway you wanted, because materia and junctions could be switched around anytime you wanted. You'll basically use the same 3 characters you want because you don't need to use the other characters at all. When you're forced to use unique characters, you basically have to use everyone, and then the player can establish connections with the entire cast instead of 3 characters. Not to mention it's more challenging when you can't basically use anyone you want.