Is this a dedicated SCUBA trip to SE Asia or are you going to the Philippines for other reasons and want to get in some scuba diving? If you can chose any country in this area, I would recommend Thailand or Malaysia over the Philippines. While the Philippines does have many good sites, travel, accomodations, and even costs are many times not competitive with these other countries. Even more, overall, the sites best sites in Malaysia and Thailand beat the Philippine sites (sorry to say, the overfishing and dynamite damage to PI reefs is too much to ignore). Since you are coming so far, why not go for the best in the area.
My reccos would be something like Sipadan/Mabul in Malaysia. Geat open water on Sipadan Island and superlative macro at Mabul/Kapalai. SMART Resort and Sipadan Water Village on Mabul are both good all inclusive resorts and cost about $750 for 4 nites/5 days diving. In Thailand, in November, you could base yourself in Phuket and do all the local sites there and also Phi Phi island too. Then move on over to Lanta Island and do Hin Daeng/Muang islands (One of the best sites in Thailand). You could also do daytrips or a liveaboard to the Similian/Richlue islands. There is also much finer dining and nightlife in Phuket than you will find anywhere in the Visayan Islands.
You can also see my previous Sipadan and Phuket reports on this site in the Asia forums.