We remarked at Wakatobi that the guides were so busy scouting out macro (which is excellent) that they ignore the profusion of corals, which to me is a shortcoming, since my photography backround is landscapes, not marine macro. Maybe because of that I spend time looking at coral as much as scouting for creepy crawlies on the bottom (not that I don't like that sometimes). The majority divers, I think, want to see things that can motate from point A to point B more so than stuff that just sort of sits there.
RA, even Misool alone, by virtue of its size, offers a lot of varied diving terrain. Komodo, to me, is the "mini" RA, in that you get a lot of variety in a smaller area. Wakatobi packs a ton of variety into a smaller area than the others if you consider only the diving done from what is officially known as the Wakatobi Dive Resort.
Just so we're not talking apples and oranges, when I picked Wakatobi over the other two, it was for soft coral only, not the overall diving experience ... and again, just my opinion. The argument about what is the "best" divng of the three ... that's a judgement I don't even want to attempt. They're all world class, without a doubt.