Hehehe Malaysia Tourism is having a fit being identified with Indonesia. You can only dive at Sipadan but will stay in Mabul/Kapalai (which have very nice critter sites all over the place).
For pelagics, you'll find Indonesia a bit lacking but a few sites in Komodo are good.
Komodo is also nice for critters in places like Horseshoe Bay, the Sangaeng Islands etc.
Sulawesi is more known for Lembeh Straits and muck/critter diving than big schools of fish. Most of the blacksand dives are 30 minutes from any of the resorts and have prolific critter life. There are a few corally sites on the eastern side of Lembeh Island but not too many land based ops will go out there. Bunaken and the Sangihe Talaud Islands, imho, is quaint and pretty but there are much better places in Komodo and Raja Empat.
So in my own rankings:
1. Raja Empat (mangroves, super coral reefs, biodiversity, topside with birds of paradise and Papua mainland jungle trek is awesome (beware of Malaria!))
2. Komodo (pelagics, critters, nice land excursions)
2. Lembeh (critters galore)
4. Sipadan/Mabul/Kapalai (nice mix but not as much biodiversity, primates are not as wild but cool nonetheless)