I have been to Misool three times and Sorido Bay twice, and on Mermaid I & II a few times. Not to disagree with anything that Lavar or anyone else has said, but here is my take on the comparison:
Misool:
Fantastic location with that lagoon right there and great snorkeling / paddling
Fantastic environmental awareness and commitment
Less currenty sites and therefore GREAT for divers that want that
GREAT place to relax, take days off, etc.
Good to great diving -- magic Mountain is a great site - one thing that keeps it great is that they limit the number & time of divers, thus the mantas get their own time there, too.
Misool resort has first dibs on Magic Mountain. They can (and sometimes do) prioritize themselves over LOBs if their guests want to repeat MM
Sorido Bay:
Has more currenty sites, as they are in Dampier Strait
At the same time, the DMs really are hesitant to take divers to currenty sites including (and especially) Cape Kri. Been there twice and had a really hard time getting them to take us there when the currents are running. Seems like the DMs just are not comfortable with it. Other sites same result -- they want to go at slack tide or on the lee side only. (And we asked, multiple times, on both visits, to go to high-current sites).
No diving on Saturdays. Internet often off on Saturdays, too (SURPRISE!)
A forced day off on Sat means that if you arrive on a Thursday, (one of two days you can arrive, the other is Sunday) you will have ONE day of diving, then a forced day off.
An 11 days trip arriving on Thursday, leaving Sunday 11 days later, means 7 days of diving.
Good internet in the cottages (except Saturdays)
Many of the "guests" you will meet at Sorido are actually there to do work on Max Ammer's airplane projects, not for diving. It seems that many come from various Christian communities. There were a few days there in our last trip where no one except Emily and I spoke English at dinner.
Mermaid I & II:
More willing to take us to currenty sites, in fact they often do, and DMs seem more comfortable with them, esp. MM I
More Western-style food which suits my tastes
Great staff and more English is spoken by the staff on MM I or II that at Sorido or Misool (Sorido is espec bad for staff English in my experience)
MM I is better than MMII in a couple ways. Choose MM I if you can.
Personally if / when we return to the area we would choose (1) Mermaid I, (2) Mermaid 2, (3) other resorts, maybe Raja Ampat Dive Lodge as Luko keeps telling us, (4) Misool, (5) Sorido Bay.
TBH, the religious thing at Sorido left a bad taste in my mouth from this last visit. YMMV.
Hope this helps.
- Bill & Emily