We spend about ten days in Raja Ampat at the Misool Eco Resort in 2018, so we can only speak for a tiny portion of this incredibly dive-friendly country. Indonesia is at the top of our list for places to return to—it blew us away with its diversity of life, from the reef manta ray (Manta alfredi) to the Napolean wrasse (Cheilinus undulatus), black-tip reef shark (Carcharhinus limbatus), and so on, and so on.
It's hard to pinpoint our most exciting moments, but they probably revolve around the reef manta ray (Manta alfredi). We spent a lot of time both free and SCUBA diving around these wonderful creatures, and learned a great deal. First, SCUBA or free, they seem equally comfortable. Although we're both inclined to say that they were faster getting comfortable with us when we free dove: in almost no time at all, when free diving, we were able to drift right alongside. With SCUBA, they seemed more skittish.
What else? At the Misool Eco Resort, you don't even need to take a boat out for most sea life: get your fins on and circumnavigate the resort island itself. The drop-off is to an easy 25 or so metres, and flush with life. Enjoy your time!