Try KBR, when I went to Wakatobi in 2003 the DMs there went to Kunkung Bay Resort (KBR) for there vacation and raved about it.
Beware of Wakatobi - they have a nice website and extensive marketing but it is all hype.
1) The SCUBA tank air was bad quality and they don't have Nitrox, which requires much cleaner delivery systems.
2) There were only 4 dive areas, not much variety. Only one had great walls but you only got to do that once per day as it was a long 1+ hour boat ride out (only 2 boat dives per day).
3) They only permit 1 entrance point and 1 exit point on the House reef and with raging currents that is a 10 min dive.
4) There were only 4 dive masters for 30 people and Lorenz Maeder gave 2 Dr.s private dives meaning 11 of us were assigned to go with one divemaster in a cattle dive.
5) Photogrpahers came last. With 11 divers the DM insisted that photogs wait in line and only after all non-photog divers had seen the subjects were we permitted to photograph them.
6) LOTS of trash on the house reef. We were dissappointed at the number of fish traps that the local fisherman have on the Barracuda reef despite the website claims they have contracts with the local fisherman against such activity.
7) The website claims AC is not needed but they are within 5 degrees of the equator and we absolutely boiled.
8) Rats and mosquitos in the rooms - despite claims otherwise on their website. They have "bungalows" which are loosely made huts.
For $250/day, next time I'd do a liveaboard where you get a broader variety of diving, more DMs, and nicer accomodations.