Agree with Palau as a great destination - as well as the reefs there are lots of wrecks to keep the variety going.
I dove Apo Reef in the Philippines last year and it was wonderful, Tubbataha Reef is supposed to be even better. Both of these would be best from a liveaboard.
Manado on Suluwesi had amazing amounts of wildlife, but it was like diving in a washing machine - the currents were all over the place and powerful, not for the faint hearted.
Some of my mates did a liveaboard from Bali to Komodo and back on a 120' sailing schooner, with a huge range of diving conditions and a day on Komodo, they actually got chased off a beach by one of the dragons. It is a trip I really regret not doing.
On my list is Yap to dive with the mantas.
None of the diving I've done in Thailand makes me want to go back.
Let me know if you want more details.