Sounds like a great trip, I for one am jealous! Black Manta Komodo trip is amazing - in 18 years of diving, with over 20 liveaboards, that's the best trip I've done yet. (Though I hope it's overtaken by Misool Eco Resort a month from now
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As others have suggested a few more days in Bali can't hurt, perhaps instead of east coast Thailand, which at least from a diving perspective won't match up to the other areas you're visiting.
I don't know the Philippines well, but I have dived Malapascua which is a nice island, good for small (as divers rather confusingly call it, "macro", in reference to the photography terminology) stuff and above all for the "guaranteed" daily dives with thresher sharks. There didn't seem to be much in the way of medium sized fish there though - not much between little critters and sharks - but it was nice diving all the same.
I hear good things about Anilao, which is famed for macro, though on that subject I do wonder if you've considered North Sulawesi and particularly Lembeh? Good variety of diving with three distinct areas within an hour or two of each other and the airport - Bunaken for walls, Bangkka for soft corals, Lembeh for "muck" diving and incredible marine life.
Muck diving sounds difficult or gross, but once you try it you'll be a convert. I did Lembeh a couple of years ago with old friends who are all instructors with thousands or tens of thousands of dives around the world between them. On every dive we saw species none of us had seen before - blue ring, mimic and wonderpus octopus, flamboyant cuttlefish, hairy frogfish, electric clam, the list goes on and on.
North Sulawesi is easy to access - multiple domestic/international airlines fly to Manado - with a range of resorts. There's also some interesting non-diving stuff to see - Tangkoko national park for Tarsiers and Sulawesi crested macaques, the volcano etc.
