Pelagian is a nice, solid converted yacht. The diving is varied--the turnaround point is Pasarwajo, on Buton Island, which is a pretty, small city outside the National Park. We did three or four dives there, including a not-bad muck site and a trashy fishing-boat pier absolutely teeming with life, including a large colony of mandarinfish--and maybe a dozen other species. The cruise directors double as guides, and guides from the resort also rotate on the vessel. They know the dive sites well, there is varied topography, and the night dives are not to be missed (but I always say that). But I believe all
Pelagian sailings are for seven nights/six dive days, so if the Pelagian is more expensive for half the number of dive days, that's a major difference, eh? I wouldn't worry at all about the number of divers:
Pelagian has max 10 (and is almost always full), divided into two groups, so there are usually 4-5 per panga.
Damai sails with a maximum of 14, but according to the website usually 12, divers in three groups, so the chances are good that your group would be 3-4 per guide.
A couple of other considerations. The Wakatobi charter planes, at least a few years ago, were not luxurious--just cramped regional jets. But getting there is easy, and if you had time to dive in Bali, then you'd see top-tier muck, along with some good reefs, at Tulamben/Amed, plus the culture of Bali is unique and fascinating.
I'd study what
@Cali_diver had to say about the Cenderawasih/Mapia trip, especially their observations about Mapia, on a good day, being on a level with R4. A bit of Googling makes it sound very interesting. Getting to Nabire looks like a bit of a challenge, but manageable with patience, good humor, and building in plenty of time.
You've narrowed it down to two very interesting options. If the peak whale shark experience is appealing, than the longer, cheaper
Damai trip looks great (in fact, tempting).