I've been to Lembeh twice, Komodo 3 times, Raja Ampat 5 times. So, it's due for checking out other places like Ambon, Banda, The Forgotten Islands, Pulau Weh, and Triton Bay.
I've been to Bunaken, Alor, Cendrawasih Bay & WaKaToBi only once. I think that's enough.
I've been to Nabucco once. Swimming with the stingless jellyfish is interesting, but once is enough for me. However, it is worth going back to see the schooling of thousand barracudas. I will never get tired of seeing them. How to get to the channel is a thrilling sport in itself. Also, there is a site there to see thresher sharks, according to Martin. I have never seen one & I like to do it someday. Seeing the coconut crabs & cat-size fruit bats in Nabucco island are also a thrill. Before going on a 3-hour boat ride from Berau to the Gilligan's island, I mean Nabucco, it's also nice to stop by Balikpapan to visit the Borneo Orangutan Survival sunctuaries to see the endangered orangutan & sun bears.
Of course Bali is the hub, whenever I go to Indonesia. I would always go to Bali & dive there for a few days before island hopping to the other islands. I'd never get tired of Tulamben & Nusa Penida, especially during Mola-Mola season. I'd skip Jakarta if possible.