Where are you flying in from? If you can get a direct flight to Cebu, I suggest you hit the sites there. There are excellent sites around Cebu and within 1-4 hours drive from the city. You can go to Malapascua to see the thresher sharks (about 3-4 hours drive + boat ride to the island) or Moalboal (1-2 hours drive from the city). Have the resorts at either locations to arrange a day trip to Oslob for you and see the whalesharks. From Cebu, you can also take the ferry to either go to Tagbilaran, Bohol (Balicasag Island has the best sites) or go to Dumaguete (try dive sites in Dauin or Apo Island).
If you are arriving in Manila and want the most diving time, try Anilao and Puerto Galera. There’s also Subic but it’s mostly diving wrecks from WWII, not much to see. All are within 3-4 hours driving time from the Manila. Of course, if you don’t mind spending your time sitting at the airport and flying, you can fly to Cebu or Coron, Palawan (excellent wreck diving).