I've been looking into this itinerary more along with my preferences. I think I'm going to skip out on Malapascua -- it's a bit far out of the way and I'm not sure if I like the idea of seeing sharks that much to go.So you are not interested in macro/muck and wreck.
Fly into Tacloban, private/public transfer to Sogod Bay(diving), ferry from Bato to Ubay(Bohol), public or private to Alona Beach(diving), ferry to Dumaguete, transfer to Apo Island, back to Dumaguete, ferry and bus to Cebu City, public/private transfer to Malapascua(thresher shark) and finally return to Cebu City to fly home via Manila.
There are a lot of travelling in this suggestion. But you can easily leave out couple of places or add Moalboal on the return journey from Dumaguete to Cebu.
It looks like my trip is going to be focused around Bohol, Apo Island, and Moalboal. I'll have to do more research on Southern Leyte / Sogod Bay since I haven't looked into it.