Been to a few places mentioned (Manado several times, Sipadan). Sipadan is good but access is now difficult, you may only get a day or two there out of a week, rest at Mabul or Kapali (good but not what you went for). Malapascua was good, saw the thresher sharks as well. Maldives, been several times, good for big stuff, great viz, best place I know for seeing mantas. Similans up to Richelieu also very good. South of Phuket to Hin Daeng/Muang also good.
BUT
The best by a very, very, very large margin was Papua New Guinea, big, small, wrecks, whatever - sodding awesome.
BUT
The best by a very, very, very large margin was Papua New Guinea, big, small, wrecks, whatever - sodding awesome.