I would second Sipadan advice a requirement combining great diving and huts above water (Prefer Kapalai resort or SWV, while SMART/Sipadan Mabul water bungalows have a lower ratio of permits per diver, so less chances to dive Sipadan) . Sipadan/Mabul combines both blue water diving with large fish schools (one of the few places in South East Asia) and macro critter. Maybe coral would be the weak point although not too bad in that respect.
Sipadan is in Malaysia according to a UN statement, so not strictly Indonesia while it was claimed indonesian some times ago by the indo gvt.
Flightwise, it isn't that difficult to go it only takes one domestic 2,5 hrs flight to Tawau departing either from Kuala Lumpur or from Singapore. Afterwards your resort will take the transfer included in their services car ride to Semporna (1,5hr) and speedboat to the island (45min).
Otherwise if you stick to huts, Misool Eco Resort in Raja Ampat would fit but it's a long way to go.
If huts above water aren't a real requirement then the whole of Indonesia is yours with comfortable accoms and great diving : Gangga island in N/Sulawesi, Villa Markisa or Siddharta dive resort in Bali, Komodo Resort in Komodo NP, Raja Ampat resorts located on Dampier strait (Sorido, Raja4Divers), Alor Eco divers in Alor, Cape Paperu in Maluku, etc.
