It depends what your interests are.

You could fly from Manila - El Nido. Do 4 nights in El Nido and do the island hopping. The town is nothing special, but the beaches on the island are fantastic. Massages are cheap, food is somewhat cheap (but not a huge selection), and the accommodations are over priced when compared to the rest of the Philippines or Bali.

Once you are in El Nido you could check out NoaNoa Private Island. It's about an 1 to 1.5 hour van ride and then a 45 min speedboat ride. It's an alternative to the El Nido Resorts. I'm going to try and do a trip report on that in the next week or two. Several other flyertalkers have gone there. It's pretty amazing as far as relaxation. It's not uncommon to be the only guests on the island for a few days. The snorkeling is unreal there.

From El Nido you can take a flight to Cebu. Cebu has some really great activities like canyoning and swimming with whale sharks. There is also some really great smaller island not too far away to explore. They also have really great diving. You could probably see the highlights in 2-3 days. Panglao Island might have a ferry from Cebu.

I've heard great things about Coron, but if you go to El Nido it can eat up part of a day to get to/from. I've heard they have great diving and snorkeling, but the beaches are not as great.

Borocay has some really nice parts. Your money may go further for lodging. It's going to be more touristy and more than likely have the best night life.

If you are into surfing you'd want to check out Siargao.

If you are not addicted to A/C I would check out http://taophilippines.com/. They do a boat tour between El Nido and Coron. This is where you are going to find the secluded beaches and have more of an adventure.

After planning out trip to the Philippines and going in December I found that El Nido and Cebu are becoming quite popular. El Nido has been exploding as far as accommodations, but the hospitality is nowhere near what you'd find in Bali. It can take a lot of research to find where to stay and what to do.