In both cases you had America taking over Pacific Islander nations, but for some reason from what I understand when the issue of Filipino statehood came up there was a racist backlash that got them kicked out of the USA. This was also around the time of the White Man's Burden, and all of that nonsense as well. You would have thought that after decades of effort in 'civilizing' those people that they would have been allowed to remain? How come arguments about tarnishing a white nation weren't such a concern with Hawai'i if that was a problem in our other Islander territory?
Aside from looking at things from the American side, it was also that there was a strong and persistent independence movement among the Filipinos. They had fought bitter and protracted wars against both the Spanish and the Americans before becoming an American territory.
The independence date of 1946 was one that was worked out between the US and the Philippine provisional government in the 1930s. The idea had been to use the time to prepare the Philippines for full independence, beginning with the establishment of the Philippine Commonwealth government in 1935.
It was unfortunate that the cataclysm of World War II shattered much of that preparation, but the agreed on date was pushed through anyway.