Start with Bali, then Komodo and Raja Ampat (R4) liveaboards or even better Raja Ampat-Misool-Halmahera trip depending on your dates. Bunaken is good but not comparable those 3 places. Lembeh strait is a shadow of what it was due to resort proliferation/diver pressure. Wakatobi is overrated and the resort overexpensive.
Have been diving Indonesia since 1991. Over last 8 years have done about 17 trips with Grand Komodo Tours, www.komodoalordive.com
, they have 5 "boutique" liveaboards for a small number of divers and the best price/quality of service ratio in Indonesia. They can put together your whole trip including hotels, local flights, side trips etc at very good price and are great at handling the problems with flight cancellations/changes or other problems that always may arise in Indonesia.
Graham Abbott at www.diving4images
also can put together a personalized trip for you to any area of Indonesia, his specialty is catering to photographers and "critter" dives. Went on recent trip w him from R4 to Halmahera and was impressed by his ability and enthusiasm.