We are going to the Philippines for the first time in August/September. We are staying for 13 nights, arriving and leaving from Manila airport.

The initial plan is to fly straight out (and in) of Manila, how much time should we plan to catch a domestic flight?

Then the most interesting question, where should we go?
There are three places that have captured my interest:
Palawan (Probably Puerto Princesa as a a base to go see Subterranean river. Maybe a few days trip to El nido?)
Borocay
Panglao Island
Coron

Is it to much of a hassle to go between e.g. 3 of these places (with flights, and transportation from airport to hotel)? Which should we pick?

We are probably going to stay in some sort of resort for the most time (our backpacking days are over). Want some beach time, but also some experiences (mainly nature). Tips for other places? Or tips for the places I've listed?

Thanks in advance for any recommendations/tips!