Depends what you like. We just got back from Turneffe Island Lodge - I doubt a live-aboard will ever get my rave reviews again. The Lodge is on a private island at the south end of Turneffe. Most of the week, we had our pick of sites 5 to 10 mins rides away.
We saw the Nekton when we went to the Blue Hole. Looked pretty beat-up from the outside, but I know that can be deceiving. From Turneffe, the Blue Hole's a 70-90 mins ride (+/- weather). However, rather than the 20' whalers that other resorts often use, you are on a 48' cruiser with plenty of room and shelter.
The Blue Hole is a "logbook" dive. It would be a shame to not do it, just for its uniqueness. We did another 2 dives at Lighthouse - very good too!
Anyhow, Turneffe Lodge is a cut above many places (with a price tag to prove it), but I've also not been anywhere better overall - and that includes 5-star non-dive resorts.
Just my $0.02