More on liveaboards in Indonesia...
Most of the liveaboards I know here in Indonesia cost considerably more per day than land-based diving., unless you happened to be staying at an Aman Resort. Paste, you'd mentioned that the Wakatobi Resort is above your budget - I'm not sure what their costs are, but I think it would be hard to find a good liveaboard that costs any less.
Some of the top tier boats (Pelagian, and Komodo Adventurer, a new catamaran) are now charging US$300 a day. Others (such as the Kararu boat) are less, but most still in the $250/day range. Evening Star II was even less expensive, but I understand that operation may be shutting down soon.
All these boats I've mentioned are mainly operating in Komodo area most of the year, but this winter several will be rebasing to Rajah Empat (West Papua) over December-March, which is the rainy season in the Bali-Komodo area. There is a lot of enthusiasm about the diving in Rajah Empat, and if demand is there some boats may start operating there more of the year. Another interesting possibility is to find a transfer trip, when these boats are rebasing. Most of the transfers to and from Rajah Empat involve roughly two-week trips between Sorong and Kupang (West Timor), which include several days diving in the Rajah Empat area,
plus numerous stops in the Banda Sea (including Banda Islands) and Alor region. Some of these sites can be quite spectacular, and are difficult or impossible to get to any other way.
As I'm sure you're aware, there are a lot of factors to be considered in selecting a live-aboard. Safety should be number one, particularly if you're looking harder at the lower-cost operators in order to reduce costs. The fact that a boat is less expensive doesn't mean it isn't safe, but I think it's worthwhile to look into what type of vessel, its condition, safety and communications equipment on board, etc. before putting your money down.
If you're a photographer, then it's important that the boat be "photographer-friendly." Most are, but some aren't. Protected space to work on cameras adequate for as many photographers as will be on board, rinse tanks, charging facilities, etc. Another issue is the style of diving and sites. Some boats cater primarily to macro photographers, do mainly macro sites. Others are more into wide-angle stuff, big pelagics, drift dives, etc. If you have strong preferences in the kind of diving and/or photography you do, you won't be happy if the philosophy and operating practices of the people running the obat lie in a different direction.
Robert