I just got back from a trip to Indonesia which included a trip on Komodo Dancer (no need to say more since Cybergoldfish has probably said it all before) and, a bit later, some time at Wakatobi.
Wakatobi is not cheap but it IS very very good.
How good? Well, I originally booked for a 2-week trip, then extended my stay for an additional 10 days at the end of the first trip. 
OK, not much in the way of Pelagics. It's in a vast "bay" formed mostly of coral reefs reaching to the surface which mean there's not all that much big stuff passing through. But there is loads of fantastic coral on walls and slopes. Everywhere the top of the reef is just below or at the low water mark, and usually it's a vertical wall or a sloping top of a sea mount. Hard and soft corals in really excellent condition. Load of marine life.
Everything worked well for the transfers (charter flight from Bali, very convenient if you're in this part of the world, but it means you can only get in or out on 3 days in any 5 week period).
The food on the first "trip" (ie 14 days) was excellent by dive resort standards, and on the second "trip" (ie the last 10 days) was absolutely outstanding. Especially the desserts. And the fresh bread. Well, lots of the main courses were also outstanding!
The house reef is truly excellent (hundreds of metres of near-vertical wall heading down to a slope, from 1m depth down to 40+ metres) and is available 24/7 for diving. The resort is on a point and the currents on either side are usually towards the point. So a taxi boat will drop you wherever you like (in daylight) and you can drift back to the resort. If for some reason you don't make it back on the current, put up the safety sausage and the boat will come and pick you up, no problems. If you want to go at night you need to walk across the beach or out onto the jetty (but the jetty can't be used at low tide as it doesn't go far enough yet).
They also organise 2 boat dives each morning, returning to the resort for lunch. Then alternate afternoons are house reef dives or a 3rd boat dive (including 2 or 3 boat-based night dives during each trip).
Dive guides were excellent and very knowledgeable. Steve Fish knows a lot about uw digital still and video imaging, and is extremely willing to help in sorting out problems and answering questions on technique.
Problems:
- Not everything is quite as described in their promotional literature. For example, no proper "photo centre", "broadband" connection is the slowest I have ever seen and costs US$10 per hour (and was only available when the staff didn't need the office computer). I ended up organising my own transfer to the airport at the start, whereas I had previously understood that the transfer was included in the price. Not big things, but my point is that you need to ask very carefully about any specific facilities which are important to you. 
- At low tide there is only one point where you can access the water, because everywhere else the sea grass is just inches under the surface. (Can't walk across the sea grass because (1) need to protect it, and (2) it's full of nasty stinging things such as stonefish) That access point is a bit of a walk from teh dive centre, so if you are doing it after dark you have to walk quite a way with all the gear, which is a bit strenuous for some. (only 1-2 minutes walk, but still ...)
- The big dive boats (for the 2 morning dives) are too big to reach the shore or the jetty except at the higher half of the tide, so there's a bit of messing about with taxi boats. This will improve if they ever get around to finishing the jetty. 
- I ate much too much!
On the way out, I looked out of the window of the plane and realised that all the great sites I dived were probably less than 1% of the diveable sites in the area. Mostly there is no land, just reefs up to just below low water mark, so there's no obvious place to build more resorts.
I'll post some pics on the web when I have another spare moment!
-David
