I can't speak for the quality of diving (I wasn't certified when I went) but I'd recommend Pangulasian Island.

The snorkeling on the resort reef was great (lots of reef sharks and turtles if that interests you). The resort itself is nice but not luxurious.I would suspect the service doesn't compare to amanpulo (I'm scheduled to go to pulo next year so can't really compare yet). That said, you can expect to pay ~50% less so may be a good compromise.

The only annoying part (and if you have the means there's probably ways to arrange something better) is that you will have to fly back to MNL to get to El Nido airport (and then a ~20 min boat to the resort) even though El Nido and Amanpulo are probably <100 miles apart.