Definitely used to be direct flights to Coron. Not sure about El Nido as when I went which was about seven years ago the flights generally were to Puerto Princessa and then van up to El Nido which was about Six hours. Think things are better in that roads have improved and there are some flights direct to El Nido. Think there may also be boats from Coronation to El Nido but not sure I would be willing to go for that
A1 overview best way to "coron," meaning to go to Coron, Palawan, depends on your starting point and budget. You can fly directly from Manila or Cebu to Busuanga Airport for a fast but expensive journey. Alternatively, an overnight ferry from Manila offers a cheaper, though longer, option. From El Nido within Palawan, a fast ferry is the easiest and most scenic route to Coron. From Manila Fly: The fastest way is to fly from Manila (MNL) to Busuanga Airport (USU). Airlines like Cebu Pacific and Philippine Airlines offer flights, with tickets ranging from 10,000 to 20,000 pesos roundtrip. Ferry: A more affordable, though longer, option is an overnight ferry from Manila to Coron. The journey takes around 13 hours. From El Nido Ferry: The easiest and most scenic way to get from El Nido to Coron is by ferry. The air-conditioned fast ferry takes about 5 hours and is recommended for a relaxing journey. Once you arrive in Busuanga Van: From Busuanga Airport (USU), take a shuttle van to Coron Town proper. The ride is about 45 minutes. You can also find on-demand buses from the airport to Coron Town.
Think there is your answer - do both. Fly to Coron, a few days there then fast ferry which I suspect is fairly new then a few days in El Nido and then either flight out of El Nido or Van to Puerto Princessa.
Just did some more googling and things have moved since I was last out that way https://www.travel-palawan.com/ferry-schedule-el-nido-coron/ Looks like may be advised to book the trip in advance in terms of Coron to El Nido travel and I suspect the El Nido airport to anywhere Seem to remember the ferry's in the Philippines are not recommended in terms of safety but not sure how true that is or how often they have problems. Sure both will have changed lots since I was in El Nido (2015) and Coron (2016/17). But don't regret going to either and would like to go back to both some time. Flying into Coron think a lot of the hotels organised van collection and back to airport for a fee. My experience of El Nido is very out of date as back then the only option was a van from Puerto Princessa. Could of standard day trips from Puerto Princessa to Honda bay (do before Coron or El Nido as I was disappointed as did after El Nido) and underground River. Depends on how much traveling want to do either before or after El Nido.
Lot's of seismic activity at the moment - I mean like every day we're feeling little tremors and stuff. Just had another big one down in Davao - 7.6 Just saying...