I've never been to a beach quite so beautiful, except for maybe Costa Rica, but that was just beautiful in its own unique way. Getting to El Nido, Palawan (where we went, and the most popular place in Palawan), is a little bit of a hastle, thus it's not as crowded as some other places in the Philippines. We got to El Nido by first flying to Manila, then taking another flight to Puerto Princesa on the island of Palawan. From there there are several shuttle buses you can take (we just purchased our tickets when we got there), that take you to El Nido. The trip lasts about 6 hours, and I believe we took the Cherry Bus there. It's pretty cheap at only 480 pp per person ($10.30).
Once you're in El Nido there are several activities and tours you can sign up for, and we did island hopping tours A and C (the most popular ones). They were very nice, and we loved getting to see all the different islands, but sometimes they felt a bit rushed. Probably our most favorite day we just rented kayaks on our own and kayaked out to the closest island from El Nido, at Paradise Beach. It was so nice just getting to explore the island and kayak on our own time. There was a little hut selling cold beers and coconuts, but besides that there were maybe 5 other people on the whole island.
Finally, we rented scooters on our last day and went to Nacpan beach, about a 45 minute scooter drive there. It was so much fun riding the scooters and feeling that sense of adventure and freedom. I highly recommend doing this. A few of the scooter rental shops wanted to keep my passport as collateral, but I wasn't okay with this. Instead I found a shop that was okay with just keeping my ID instead. Palawan is a beautiful island, and I will remember this trip for the rest of my life. Go here if you get a chance!!