I have taken the long trip from Puertro Princesa in Palawan to Manila a few times. As I said, it is a very long trip. However, I think using the ferry from Puerto Princesa is a smart move for the traveler.
I think this for three basic reasonin
After a week in El Nido, you need a day of downtime
The trip basically pays for itself.
You get to see some of the best landscapes the Philippines has to offer
At least, these are the reasons that I normally book the trip back to Manila with 2Go Travel. It is alot better than using AirAsia in my opinion.
How does the ferry from Puerto Princesa work?
The boat will leave out of Palawan around midnight every Saturday evening and it will get into Coron on Sunday afternoon. After about two hours in Coron, the ferry will continue on to Manila. It comes into Manila about six in the morning on Monday. It is basically one day and two nights on the boat.
The reason that I say it is free is it basically pays for itself. Currently, the fare is about P1500. If you figure that you would pay P1000 for two nights staying in a hostel; your trip back to Manila cost a net of P500.
An island hopping tour in Coron for close island is over P1200 and you get to see the whole group from the most outer point as you come into Coron. Oh, you leave Coron dodging all the beautiful scency at sunset. What a great time to see the beauty of the Philippines!
What about from Manila to Puerto Princesa?
It leaves Friday evening for Coron on Saturday morning and then comes to Puerto Princesa about an hour before they leave back for Manila on Saturday night.
I do not use it to come down to Palawan for the reason of the schedule. I do not want to come to the city in Palawan at 10 at night. I like the overnight trips and arriving early. It is a personal thing. Also, the savings on the accommodations is really not there for the trip down.