I am arriving a little late to the party but perhaps some of the info I share can be useful to others as well:
Re: looking for whale sharks. I did Southern Leyte looking for whale sharks at the beginning of Philippines diving trip and while I saw a few, that experience was dwarfed a million times by my experience at the end of my trip in Tubbataha. We saw soooo many whale sharks on our dives. I would say an average of 1 or 2 each dive, every other dive. And on a few times, it wasn't simple pass by like I experience in Leyte, but them circling around us for half of the dive! Hopefully you have a similar experience in Tubbataha as I did (I went the second week of April) - we had a lot of luck with the WS on the eastern side of both atolls though I am sure that changes. It might spoil you for the rest of your diving in the country though (as good as it is elsewhere, I'm glad I did Tubba last - also know some people that went on the Stella Maris and really enjoyed it). Also don't miss the hammerheads, mantas and a million other (sizeable) reef sharks.
I did four internal flights, all with PAL. I initially booked a flight with Cebu Pacific but they cancelled the flight slightly last minute and offered up a very unsatisfying alternative (they reimbursed me and I booked with PAL instead). PAL was early/on-time on 3 of the flights and devastatingly late leaving Puerto Princesa though this was blamed on Manila ATC so avoiding that airport often takes a lot of the hassle out of Filipino air travel (though not always!). The weight restrictions on PAL were unevenly applied. For my checked bag I was a few kilos over the limit and was only asked to pay extra on 1 of my 4 flights (it might have been because those other flights were not full, or just had a nice agent? no clue) though the cost was not a lot since they charge a certain amount of pesos per kilo over. The size of the plane had no bearing on this as the one time I got charged I was on the larger airbus 320 (versus the props I took). No one ever sized or weighed by carry-on bag but I use the more conspicuous duffel (versus a trolley).
Malapascua was great but the only diving that really impressed me was with the threshers. Kalanggaman is a great island to visit but I found the macrodives nearby to be underwhelming (but I also found Gato Island underwhelming and that is what people sometimes rave about). Its a very cute island though with a nice dive community so I'd recommend doing early dives and enjoying the rest of the day at the beach, getting massages and enjoying ocean-front happy hour! For next time of course...