I've been to Indonesia several times over the last 9 years and have just spent a year working on a liveaboard there (Damai).
The options for diving are all superb, whether liveaboard or resort and its often worthwhile to do a combination of the two to maximise the places you visit and types of diving you can do. Agree with Dirtfarmer... be wary of addiction! Travel between islands is fairly straight forward but does take a little bit of planning. Main hubs are Jakarta, Bali or Manado. From any of these getting to more remote places involves 1-3 domestic flights
Raja Ampat is certainly one of the most diverse dive areas of Indonesia. mantas, sharks, fish schools and critters like nudis and pygmy seahorses. Best time of year / when most of the liveaboards operate is Nov - May. My personal fave time is March. RA is also one of the most popular so you will see other boats aand divers about, but usually there is avery good co-op between operators to avoid dropping divers on the same sites.
Komodo - again a top spot for diversity. Liveaboard would be my preference as I feel you get to experience more of the region, but there are a few quality dive centres in labuan Bajo offering day trips. Think now RA has surpassed Komodo in popularity but Komodo still has many boats and operators so very likely to see other divers about, again with co-op between operators this is usually avoided
Triton Bay - newish dive area but great for critters, colourful coral reefs and good chance to see whale sharks. Not so easy to get to but then not many other divers around! Triton Bay Divers is the only resort option, and it is lovely. But several liveaboards run trips there as part of other itineraries (Damai does RA and TB, Ambon to TB for example)
Lembeh - mostly resorts and plenty to choose from. Awesome critter diving, but some lovely corals too. Very easy to get to with direct flights into Manado from Singapore.
Bali - day trips to Nusa Penida for mantas and mola mola, great critter diving around Tulamben off the north coast or Menjengan in the West. Plenty of diving areas. Some liveaboards start komodo trips here, but predominantly its resorts and day boat boat diving. Loads of great operators to choose from.
Ambon - known for critters but also some lovely reefs and some bigger fish hang out on the northern side. Maluku divers just closed but there is Dive Into Ambon and a newresort will open soon (Maluku Ambon Divers). Can be quite dirty as trash flows in and out of the Ambon bay but the critters are wonderful. Some liveaboards start of end here as part of a longer itinerary.
Banda Sea - Liveaboards take divers across the banda sea, usually starting in Ambon or Maumere, so the reefs you are diving are extremely remote. banda island is steeped in history with a lovely fort and nutmeg plantations. Good for big fish, dramatic seascapes huge barrel sponges on dark sand, seasnakes (though they creep me out!), october is a good time to see hammerheads.
Alor - fabulous for critters and not as popular as lembeh or ambon so my experience there is really few divers and great variety. can see some big stuff like hammerheads, reef sharks, mola mola and mantas. Plus there is a large pod of dolphins that hang out in the pantar strait. Some liveaboards include Alor in a Banda Sea itinerary so good option if you like variety (look for one departing from or ending in Maumere) there are a couple of decent resorts in Alor. Flights in are getting more frequent too.
Cenderawasih Bay - only liveaboards at the moment. Great for whale sharks and some interesting wrecks. Mapia Atoll is awesome for big fish action but you'd need to check if your liveaboard is going there.
There is also bunaken, Gili Islands, Lombok, Forgotten Islands.... but i've not been to those, just writing to illustrate that indonesia has many choices and once you startits a slippery slope!
My next trips are
March/April 2019 - Triton Bay to Raja Ampat (on Damai) followed by 6 nights in Lembeh (Dive Into Lembeh Resort)
August/ September 2020 - Komodo from Labuan Bajo to Bima Bay (on Samambaia) followed by a stay in Bali (probably Tulamben but maybe Menjengan)
October 2021 - Banda Sea and Ambon .... still planning!
