...I think diving in the Philippines pertains more to specialized interest diving, I don't see any other places in Indonesia that would cater for so many and easy to spot whale sharks as in Donsol or Oslob, such a huge sardine school than in Moalboal, as many chances to spot thresher sharks than Malapascua or an array of various sharks including tigers and hammerheads than Tubbataha. Also when looking for really interesting nudibranches, Anilao and Romblon are on the top list.
Another good thing about the PI is that diving has got cheaper than in most of Indonesia (incredible how the prices rised in Bali and N/Sulawesi these past 3-4 years) and that I find better and more involved dive guides in the PIs than in Indonesia.
... But overall my favorite spots are still located in Indonesia... just to prevent from too broad comparisons...