See the threads on Manila airport for more information on how long it takes to get from domestic to int'l or vv. In general it's much like the rest of the Philippines - slower than you plan on. Give yourself ample time. And transferring between places within the Philippines easily takes a full day, so be prepared.

Palawan is nice and has the remote feel. You can fly to Puerto Princesa (PP) on regular airlines and then bus to El Nido (6 hours or so) or take a van (3-4). The subterranean river is a bit far from PP, so it takes most of a day and is hard to go from there straight to El Nido. Besides the river though I don't feel there is that much in PP. There are some nice small towns in between though if you like to find those type of places.

El Nido requires a small flight that is harder to book in advance. Lots of cliffs, coves, island hopping. I think Tao is highly overrated, but ymmv. You can hire a small boat to take you to a small beach to camp for a few dollars if you want that kind of thing.

Coron has the better underwater life, i.e. snorkeling and diving. Some great shipwrecks. The boat from EN to Coron or vv looks uncomfortable to me and frankly looks a bit risky to me. But many people do it and it is a full day.

There are no flights from EN to Coron. But from PP you can go to Cebu. (per astrophsx my info is old, and you can go to Cebu from EN)

From Cebu you can take a bus or taxi several hours south to Oslob for the whale sharks. Some people don't like the unnatural element, but I liked it a lot. There are some nice resorts on Mactan Island (where CEB is located). Or you can take a ferry from Cebu to Tagbiliran then taxi to Panglao. A bit more touristy, pretty good beaches, some great snorkeling and diving if you get out to Balicasag. Panglao does have good access to the Chocolate Hills and to the Tarsiers.

I've not been to Boracay, but it is definitely popular and beautiful in the pictures. Average diving and snorkeling from what I hear.