I agree that it would be great, but only if you could guarantee proper administration. With governing bodies, you'd end up with worthy contenders being denied title shots their whole career, and favoured fighters like Chavez Jr having the system rigged in their favour. With rotten organizing bodies, a one belt per division system might even be worse.
Obviously the sport would be a lot better off if you could have it run by an NFL or NBA type organization, but boxing is harder to organize than football or basketball. The outcome is subjective, for one, and you can't really set up leagues or championships in the same way.
Any governing body would have to have supreme power and it would have to be backed 100% by the government. Otherwise the promoters will end up back in charge.