Dan
Contributor
For a trip of a lifetime, first I would recommend a liveaboard in Raja Ampat, and if you have time I highly recommend you add a short stay before or after in Lembeh (Muck /critter diving). I prefer "before" so I can get my dive mojo (weights/gear etc.) before I get on the boat, but if you think you and your buddy might need a few dives to get your buoyancy right you might want to do this at the end. (this would have to be from Oct/Nov- March-ish) This will give you a taste of the best of Indonesia. And I guarantee you will want to come back.
For the other part of the year the second choice would be Bali and then a Komodo Liveaboard. Tons of info on the Indo board so just start searching and you will find lots of great advice. @Dan_T will probably throw in some great videos to entice you!!!
Indo is quite a bit different than the Carib. You don't have that vast see forever visibility. Not to say that you don't have good viz... but with currents and nutrients in the water you have lower viz but incredible amounts of fish. So thick with fish sometimes you can't see the surface. So it is a give and take.... but I would take all the fish any day!!
Since you mentioned it, here is a picture of bump-head parrotfish that I took during diving in Tulamben, Bali. You will see them in school early morning dive (before sun rise), when they are just waking up & searching for breakfast in USS Liberty wreck.