Yes!
We spent 3 weeks diving at KBR several years ago when the property was new. It has changed hands a couple of times since and I'm told that it's back to what a dive resort should be.
There are a couple of live aboards that are doing Bunaken and Lembeh now as well.
I've heard that Hairball is no longer the spectacular muck dive that it once was, however Police Pier is pretty much guaranteed for a wonderpus. Also, flamboyant cuttlefish were quite prolific recently. Angel's Window was a nice 'pretty' reef.
But.. having been to Wakatobi... how can you go wrong by going back?
If Adventure Komodo was still running, that would be good. I have heard positive reports on Pegasus, a live aboard out of Sorong. Lots of places to see in Indo.
-Rob