Too many independent cities, the wealth isn't able to spread to the rest of the provinces.
In the case of Cebu. The city and the province have seperate jurisdiction and separate budgets, although the government of the province resides in the City. To me, that doesn't make sense. The city should be subserviant to the provincial Governor like here in the U.S.
The wealth of the city remains in the city, the problem is that the city itself is too small to handle it's own problems like waste management, and metropolitan traffic. Once you cross over to Mandaue City, it's a different police force and traffic authority.
Cebu City would rather be part of the province, so some of it's waste management problems can be addressed by moving the waste out of the city, which does not have space for it, and the revenues of the city can be dispersed to the other parts of the province.
This is part of the reason why NCR is so bad. Too many independent cities with independent budgets, different police force, traffic authorities, waste management problems, and they are too small to solve it by themselves. This is why they created the MMDA(Metro Manila Development Authority) with the head acting like a governor, except the person is appointed by the President not elected.
Rather than have an MMDA with limited authority. They should have NCR as a province, MMDA chairman replaced by an elected governor of NCR, and have the cities be component cities of the NCR province rather than a collective of independent cities. The mayors will all be subserviant to the governor.