Wakatobi is surprisingly easy to get to.
I booked a flight to Bali (SFO->Taipei->Bali) on EVA Air and spent a few days exploring Bali. On the morning of the 9th, Dave and I were picked up by a Wakatobi driver and shuttled to the domestic terminal at the Bali airport, where we were met by Wakatobi staff members. We spent some time in a comfortable lounge, and then boarded a chartered flight to the airstrip on Tomia Island (passing all sorts of beautiful little islands and mountain landscapes on the way). I spent some time in the cockpit with my 15mm fish-eye lens, taking photos and chatting with the pilots.
After arriving, we were shuttled by van through a local village to a dock, where waiting boats took us for a short ride to the resort. Our luggage met us in our rooms. Piece of cake.