Boracay is very good. But given that you want more than a beach vacation, I second the Panglao/Bohol suggestion. I was there a few months ago. The beach itself is very good, not great. But you also have some day trips, like snorkeling around Balicasag or swimming with the whale sharks over at Oslob (not the best ride though, check reviews to be sure you want to do it), the tarsiers, as well as the chocolate hills. You can take the ferry from Cebu or just get your domestic flight into Tagbiliran. If you want to do a bit more, you can head back to Cebu and go to some places around that island quite easy.

Note flights to MNL from the smaller airports are quite late sometimes. Lots of posts recommend getting into MNL a day before your int'l flight, although if you have 3 or 4 hours or more advance arrival back to MNL, I usually feel that is enough leeway.

ETA: I went to Palawan and it was ok, but long drives between places, not much sea-life. Very nice views, and some fun island hopping. I flew out from El Nido cuz I couldn't take the long ride back to Puerto Princesa. And the boats from El Nido to Coron I was hoping to take were not comfy (wooden benches for 8 hours) and looked, um, not seaworthy, to say the least. But to each his own. If you like that idea, Tao Adventures does a fun camping/snorkeling tour from island to island. They're booked well in advance, but lots of people like it a lot.