PAL to PAL connections at MNL are the easiest since you won't have to change terminals. Same with Cebu Pacific.

If the beach is important to you, be careful how you choose your hotel. We stayed at the Hilton, and the beach and pool areas were not fine, contrary to a trip report you may find elsewhere on Flyertalk. Small overcrowded pool that is in the shade most of the day and an artificial beach area right next to a Marina and the associated dirty water and air.

The Shangri La has the best beach area I've seen but there may be other more boutique types of properties that also have nice beaches.

If it were me, I would spend a day or two in Cebu City, as there are attractions, sight-seeing and shopping options, and then spend my beach time on Bohol (a short ferry ride away) - Panglao island having some fairly decent beach and diving resorts.