I think if the Filipinos got what they initially want in the Precolonization era and got self determination because the Spanish colonization got delayed because Portugal gets unified with Spain in early 1500's and because of the Spanish inheritance of Mollucas and Timor.
I think:
Luzon: A Hindu Neo-Majapahit state after the expulsion of the Bolkiahs, the people of Luzon actually wanted to be ruled by hindus rather than a muslims, Luzonians will be mestizofied(mixed) with the Hindu Malay/Javanese refugees from Majapahit.
Visayas: Could fall to Portuguese or Spanish rule.
Mindanao: Maguindanao Sultanate, a Hindu-Muslim hybrid state.
Sulu: Continuation of the Sulu by the Muslims..
I think this is the best thing that could have had happened in the Philippines