I’ve been to Komodo 2x (Mermaid II 2013, Adelaar 2019), Raja Ampat 2x (Mermaid I 2017, Damai I 2019), Bangka island 2014, Bali 2018. Raja Ampat is really in a league of its own, from the marine life variety, big and small, to topside scenery. Komodo is a close second, but the emphasis is a bit more on big animals, less macro. Cannibal Rock that others have mentioned is (was?) an incredible site, I dove it 3x, one a crazy night dive, and it’s one of my all time best. I’m shocked to read that it was bombed… south Komodo waters are colder, a bit green, and lower viz than in the north. If you’re limited to just the south, and Cannibal rock is gone (and who knows what else) I might focus on RA instead. Manta sites are good in Komodo, but you’ll most likely see mantas in RA too. Komodo also got much much busier over the years, I noticed a big difference between 2013 when we hardly saw any other boat in a week and 2019 when boats were left and right with fuel spills on the water. Marmaid boats are wonderful, especially Mermaid I hits the sweet spot. I loved the food. And you should definitely do a liveaboard trip in RA - the park is so big, you need a boat to see it.
Depends what you’re looking for, but for me Bangka was a bit of a downgrade from Komodo (though that’s comparing to the whole park, not just south). Really lots of weird macro, multiple species of Pygmy seahorses, electric clams, frog fish, but nothing bigger than a Napoleon fish. Some good reefs, not crowded, I stayed at Murex (on Bangka) and the setting was basic but really dreamy. Nice snorkeling right in front too.
Diving in Bali is only good for macro, no good reefs left there. Lots of nudibranchs though. I like Bali just for relaxing - do some yoga in Ubud, visit the rice fields, go to a dance show etc.
If you’re heading to RA, then arriving to Jakarta would be more convenient since you can get a direct flight from there to Sorong. Maybe fly into one and depart from the other if you still want to go to Bali?