Yes, El Nido (and the 5hr van ride associated with it from PPS) was very worth it.

There are no chain hotels, which is an upside to any destination from the getgo in my books. There are lots of nice smaller hotels.

Stay in town, and take all the day trips (A,B,C,D) for snorkeling. That will fill up 4 days in itself. Tour rates have recently increased to about $30 for the day. When I was there in 2013, it was about $20 .. progress eh.
We stayed here for about $40 a night in the deluxe room overlooking the bay, there are lots of other small hotels in town (and out of town)
http://www.tripadvisor.ca/Hotel_Revi..._Mimaropa.html


You dont have to stop in PPS, the shuttles go directly from the airport to El Nido. Just make sure not to book your outbound before noon, as the earliest van back goes at around 5am.