I believe the whale shark season starts in December. I've been to the philippines 4 times even after visiting places like fiji (liveaboard), sipadan, honduras, mexico, and I keep going back. Here is a quick run down:
Anilao - easy to get to from Manilia, compentent dive operations (generally). Little or no big fish. Reef fishes on the farther out/deeper reefs are pretty good. You should see a good assortment of nudibranch (probably because no one has figured out how to prepare them for lunch...
Bohol - Can be great, like Pamilaian/sunken island the best. Lots of choices of who to dive with and places to stay. Avoid the house reefs, pretty torn up. Lots of sea snakes, good schools of jacks, turtles, 4 different frog fishes over a 4 day period.
Dumaguete(Dauin)/Apo Island - probably my favorite. I saw more "critters" here than any where else I've been. Devil fish, ornate ghost pipes, hairy frogfish, flashlight fish, schools of clownfish (really), turtles, juvi emperor angels, juvi sweetlips (the brown/white one), 2 different types of sea snakes. I could go on and on, saw quite a few of my "want to see" items here over 5 days. I'm going back for 18 days in Nov, 9 of them just to apo.
Moalboal - great deep wall at Pescador island. This is more of a resort town if that is what you are interested in doing. Diving was pretty good, better than Anilao, but not as nice as Bohol/Dumaguete. A lot of the diving is very deep, 150-180 is not uncommon based on my experience.
Malapascua - famous for thresher sharks, haven't been here but friends tell me it's pretty good if you see the sharks, otherwise... well lots of rubble from the dynamite fisherman.
Coron - famous for the wrecks, if you are into that I hear it's as good as if not better than Truk. I have not been to truk, so that is based on hearsay.
Stay away from Mindinao, good diving, but a lot of anti westerner feelings in various places. You would probably be ok, but the diving isn't worth the risk right now.
Palawan - diving is so so if you are not on a liveaboard out at Tubbataha.
As a general note, I noticed the trend towards deeper diving in the philippines compared with other locations. Don't be surprised if you stop at 130 while your DM heads to 150 with the rest of the group (happened several times).
Good luck, I hope you enjoy your stay.
Dave