If you have more time to see the rest of the country, the traditional choice is Palawan.
I like Palawan, but I don’t see it as a high priority compared to Boracay and Sagada.
If you really want to go to Palawan, I would suggest you go to the Northern part, in the island of Busuanga. Near Busuanga, is Culion island. This used to be a former leper colony, so is not high on the tourism list, but this is where it’s charm lies. The people here are more authentic and you’ll probably run into no other tourists but yourself. They also have a fascinating museum about its former past located in a college on a cliff (awesome!)
Get off Culion and you can go to the baby Boracays. Imagine whole, little island Boracays all to yourself. You can snack on giant clam, which might be endangered, but the fisherman I met had a whole farm of them (which I saw with my own eyes) which kind of cut down my guilt 😉 The island I stayed on was Malcapuya. You could stay there overnight but I only stayed for the day.
Now if you really want to see old school Marcosian Palawan, you can head off to Puerto Prinsesa. The two or three places to see here are the penal colony, underground river, and the art commune. There’s also a famous resto here, Kalui. I ate the stingray in coconut milk. I know this all sounds like sin food, but in Palawan, what is supposedly endangered is still plentiful and unthreatened. Try eating also at the former Vietnamese refugee camp. The food there is the best Vietnamese you can get in the country.
You can also eat mangrove worm (tamilok), which I have yet to try. Looks like a tasty oyster actually.
I’ve never gone to traditional backpacker area of Port Barton, but I would like to see it for curiousity’s sake someday.
I’ve been to El Nido but was underwhelmed.
I prefer the wrecks of Coron (also in Busuanga in the North), and if you stay in Coron, I suggest Discovery Divers. Check out Barracuda lake and Kayangan lake (haven’t been to the latter, but supposedly the freshest lake in the country).