Wakatobi might require an early (1-2 years ahead) reservation, especially for a larger group - you can check their website for availability for your travel dates. Also don't leave out Lembeh Straits or Manado in your vicinity. A little further is Sipadan - you'll need to get to Singapore or Kuala Lumpur and on to Kota Kinabaru, early morning flight to Tawau, followed by a land trip to Semporna, where you can stay or move on to Mabul (more expensive). Sipadan lodging is closed but can be accessed via Mabul or Semporna. You can also consider Phuket and the Maldives (both 3 or so hours' flights from Singapore, which is 3 hours from Bali). Both can be dived land-based or via liveaboard.
Dive safely and enjoy your trip!
Dive safely and enjoy your trip!