For those that have dived Bunaken and Wakatobi how do they compare in relation to marine/ coral diversity?
Note: These are "my" observations ... YMMV.
We saw more schools of fish in Bunaken (2009) ... definitely larger fish population, but no pelagics other than a few sharks, usually deeper and out in the blue. Some divers do see a few more pelagics. Good turtle population in some locations. Very nice stony coral gardens in the shallows above some of the walls. Fair amount of soft corals. Always some macro life to be seen.
At Wakatobi (2007), fewer schooling fish, but still a good variey of fish. Pelagics were uncommon. Hard and soft coral, gorgonians, etc. in massed profusion. Every color and species you can think of (more have been identified in Raja Ampat, but it's not like you can see them all). I have told people that the visual experience at Wakatobi is like Alice in Wonderland on acid (just a guess of course, not having any real experience with that). Lots of unusual critters, great macro. Fair turtle population. The biggest morays I've ever seen in my life!
I'm glad I've done both, as they have many differences, and are both first-class diving, but if I had to pick one for total richness and variety of marine life over the other, the biggest sensory "hit", it would defiitely be Wakatobi. I have also read (but cannot confirm myself) that fish populations in Wakatobi increase yearly as the reefs there no longer have the local fishing pressure they had before the resort existed.