I stayed in both WaKaToBi Resort (2009) & Misool Eco Resort (2013). Both resorts costed me an arm & a leg then (~$10K for a couple divers). WiFi’s were sucky then. I hope they are better now.
As far as diving, I’d go to Misool hands down, especially since you will be in Raja Ampat already. No big fish in WaKaToBi Resort then. I was disappointed. Coral wise, Misool is known for the soft coral. Also, you can see Oceanic Mantas in Misool (Magic Mountain), along with some sharks (blacktip, wobeggong, walking shark, etc.).
My recommendation for the second week will be Bali.