My parents are actually from the Philippines. It's interesting...Filipino (Tagalog) has a lot of Malay words. Same ""Malay race". Many national heroes of the Philippines had a dream of a "Greater Malaysia" because Malays were divided by political history.
I know you could say Spanish colonialism, but from my understanding Filipinos accepted Spanish rule very quickly? Also why did Islam not spread nearly to the extent as in the other Malay countries?
In what ways do you mean that the history of the Philippines is so diverged from Indonesia and Malaysia? One could argue all three diverged from each other because each was colonized by a different European power. But I would like to know more specifically what you mean by your question.