El Nido is tricky. I highly suggest when you do your research to read the negative reviews first. Go for the ones within the last year. The accommodations in that area of the Philippines are new to the hospitality industry.
We stayed at El Nido Mahogany Beach Resort. It has about 7 or 8 villas. It's on the beach, but not really a beach you'd want to swim at. The positive is that it is quiet, beautiful, and you can take private boat tours right from your doorstep.
That's a video where we paid to have a boat take us to a nearby beach where we had it for the full day to ourselves. I think only 2-3 people stopped by. All accommodations in El Nido are overpriced for what they are, but this one we thought it was money well spent. Also, you do NOT want to stay in the town. You want to stay to the north or south. I think it was $1-2 ride into town (8 to 10 mins) from the resort. You also have the El Nido resorts that are all inclusive and are usually $450+ a night. The food is mediocre and the over the water villas are okay. They include free island hopping which is nice. I did a trip report for the private island near one of the El Nido resorts. Was one of the best places I've ever visited.
Cebu I stayed at Malonzo Pension House in Oslob for the whale shark experience. It was very basic, but I would highly recommend it. For the canyoneering I took another FT'ers advice on his trip report (
http://www.flyertalk.com/forum/trip-...d-el-nido.html) and stayed at Marcosas Cottages Resort in Moalboal. Check out his trip report as he also stayed at a place called Villa on a Cliff for a few days that looked pretty nice. There is also a small island off of Cebu I believe on the south-east side. I guess it depends on what you want to try to get out of your 2 nights in Cebu. That same trip report has some options of Boracay.
In Manila the best place IMO is the Hyatt City of Dreams. There are also some options that are new where you can stay in the terminal. If you have less than 16 hours in Manila this is a good option as it will take you a long time to get out of the airport and to a hotel because the traffic is so bad. I think it took me around an hour to get to the Hyatt even though it is around a mile away.
PM me if you have any questions.