Manila
I would completely skip Manila. Fly in, stay the night at the Hyatt City of Dreams, then fly on to your next destination in the morning. Seems to me you will land in Manila and want to spend one night to relax. I don't know if Banaue rice terraces is a day trip? It looks like an 8 hr drive one way. If there is an airport I assume it's going to add on a lot of time and cost to your trip. We've done the rice terraces in Ubud, Bali and I thought it was great... but I wouldn't want to spend more than an hour or two in a rice terrace exploring.

Palawan
Most people would agree that you will want to go to Coron for diving. You can look up "Lost LeBlanc" on YouTube to get an idea of what it is like. For beaches you will want El Nido and that is an 8 hour boat ride as there are no direct flights that connect the two.

We took the flight with Air Swift from Manila to El Nido (not that cheap). From El Nido we took a ~1 hr van ride to TayTay and then a boat ride to a private island. I detailed it in this trip report: http://www.flyertalk.com/forum/asia/...ip-report.html

The snorkeling there was unreal! I think it was superior to diving in Coron, but check out the videos of that experience in the trip report and look up some diving videos in Coron to compare. From that Island we went to El Nido for 5 nights and did island hopping which was a blast. I would say only the private island had good food... the rest of the Philippines was meh.. So focus more on the activities.

Cebu
I would not miss Cebu. In fact.. I would skip Boracay for Cebu. There is a direct flight from El Nido to Cebu. The top two things are:

Canyoneering

Swim with Whale Sharks

I used this trip report as a start:
http://www.flyertalk.com/forum/trip-...d-el-nido.html

I also used Lost LeBlanc's videos on YouTube to research other islands like Bohol. I would highly recommend that you check out his recent videos from Boracay to get a real feel of what it will be like. You will want to google to see when peak season is and when locals do their traveling as you will find that the rates may go up slightly but that the hotels with the highest reviews on TripAdvisor may only have 10-12 rooms and can fill up quite quickly. We went for Christmas and it was quite busy then, but I think March/April was when the locals traveled... can't remember. You will also want to take a look at what award availability is if you are doing an award flight to get there.