Bonaire is nice, the shore diving is easy, and it's a good place to get away from it all. But I've found the diving looks mostly the same after a bit. Much as I like little critters, I also like variety and "views." There's some areas that have a a little different UW scenery and and topography, but they're not the ones some boats seem to frequent. I've stayed at Sand Dollar once and Captain Don's a few times. Also haven't seen much of a selection of good food/restaurants, but I haven't been there in quite a few years and I keep reading that it's better.
I think GC has more variety in the diving, and it's easier and cheaper to get to. (Of course you can easily spend all those saving once you get there!) More civilization, for better or worse. I've usually not been too impressed by dives on the West, often very crowded, kicked up, or overdived sites. But North/East/South are great. It's harder to get to all the different diving on GC, certainly not from one place, and have it be convienient too - there's no really nice place to stay, with nice boats, where I can walk out of my room and get on a boat (or at least van) to wherever, or jump right in the water and have a good shore dive. (Yeah, I know, I want everything.)
We liked Cobalt Coast a lot, and were pretty happy with Dive Tech. Lovely place, away from everything, yet not too far to drive to shop, eat, whatever when you were in the mood. One problem was that it was rough when we were there (April 02?) so we were never able to shore dive from Cobalt Coast and had to drive to the Turtle farm shop all the time for shore diving. They advertise the facilities at Cobalt Coast, but don't go out of their way to mention they might get blown out alot. I did figure that was a possibility on the North wall, but had hoped April was late enough - oh well. We got driven to various locations every day to get on the boat, and most of the boat dives were to the west, again because it was rough. Hauled gear all over the place that week. From what I saw, I do think Dive Tech was a bit too conservative on declaring the North wall too rough all the days they did; they were catering to the least experienced people. One of the DMs admitted this to us. I might try there again at a time when there's better odds of it being calmer, maybe split the trip and try OF on East end.