I traveled on PAL Express recently (Dec-Jan) MNL-KLO and back and overall it was fine though both flights were delayed by several hours. At the time at least, there was a lot of negative reports about Cebu pacific delays, cancellations, overbooking, and we saw the massive lines firsthand at MNL Christmas Eve and on the return from Kalibo (some passengers had been delayed a day+). I don't know if the situation was due to the holiday season or routine but was definitely glad we weren't traveling Cebu Pacific.

Safe travels and enjoy the Philippines!