As mentioned by others, for lack of competition, the PAL direct flight is not cheap. There are numerous ICN-CEB flights, so that leg is cheaper. Cebu Pacific can go as cheap as $400 or even less for that leg. You can also try JetStar from NRT to MNL for about $450, and MNL-CEB is often less than $100 round trip and can go below $50 if you grab a promo. For about $550, I would go with Korean Air (via ICN), Asiana (via ICN) or Cathay Pacific (via HKG). Yeah, there's a layover, but service of these airlines surely beats PAL.