I have to echo what others have said. I have never been to Bonaire for a few specific reasons, but I would disagree with it being the yardstick against which all Caribbean diving is measured. I think Bonaire does a couple of things really well...preserve their reef, and make it easy for divers to shore dive as much as they want in a wide variety of locations with relatively few obstacles. For those who believe the metric by which to measure a dive vacation is the number of dives on a quality reef divided by the number of dive days, Bonaire is certainly hard to top. For macrophotography buffs, Bonaire is similarly at or near the top of the list for many.
But for those who value other qualities in a dive vacation, such as relaxation, variety in dive terrain (walls, shallows, swimthroughs, etc), and bigger stuff like turtles, sharks, rays, etc. Bonaire doesn't stack up so well. For me personally, I won't go to Bonaire until I can go at least a year without reading about somebody getting stuff stolen out of their truck at a shore dive location. That is a very simple things to combat on a small island. The locals know who is stealing the stuff there...if the police wanted to catch them, they would. The fact that they don't suggests to me that they see value in a cheap black market for items stolen from tourists...which really turns me off. I also value my relaxation over the sheer number of dives I can get in one week. If I have to choose between doing "valet diving" on Little Cayman and hardly ever touching my gear for 2-3 dives in a day versus schlepping my own gear all over and back in order to get 1-2 extra dives in a day, I will choose LC every time.
I am sure somebody who loves Bonaire will come along and give the counter argument here soon. It really is about personal preferences, and what people are looking for. For a certain sector of the dive marketplace, a high # of dives with a wide degree of personal freedom, and a quality reef trump other considerations, and for those folks, Bonaire is pretty close to Nirvana.