I made a short video on how to get to El Nido from Manila:

I would highly recommend skipping Puerto Princesa if you are able to. From everything I've heard it is a bit exhausting to take a 5-6 hour van ride to an from El Nido.

You could fly to Cebu and do 3-4 days there. You'd be able to go diving, snorkeling, see the whale sharks, do cayoneering, etc... There are typically late flights that depart the same terminal that go to Cebu. Then you could take the direct flight from Cebu to El Nido. You would then have the option of doing the flight from El Nido to Manila or taking a shared van to PP.