Seems there are a lot of good dive operators in the Galapagos. Apparently there is some talk by the Ecuadorian government about not letting the liveaboards do shore excursions next year, but can't get a straight answer on that.
There are apparently only a handfull (less than 10) operators that have the license to do the outlying dives (Wolf/Darwin). Hughes, Agressor, Quasar Expeditions, etc. all have nice setups for doing the outlying "islands". All of these trips are pretty pricey ($4500+), but the boats seem to be nicely rigged.
One item to note, is that on most of these boats, you are diving out of a hard-bottom zodiac. They simply can't take their boats close to Wolf/Darwin due to currents, surge, etc. The fact you're doing back-rolls off of support craft seems to slip most people's mind (and the various websites for the liveaboards), but it isn't a big deal, either. I haven't been (yet), but understand it can be quite an experience reboarding a zodiac in heavy swells. But hey, you're there to see whale sharks, right?
But I did do quite a bit of research on all of the liveaboards. Except for the occasional whining of some posters, all of the operations seem to run a good trip, and pretty much pamper you with good food. Seems they try and nickel and dime you with add on fees, but if you can afford it in the first place....
One thing to check is whether or not they have Nitrox. Some of the boats, it's first come, first serve. Don't know how tolerant you are of compressed air, but you'll be doing 4 dives in a day, so Nitrox sure is nice on the body, even if your MOD is about 108 feet (on 32%). That's the only glitch I have seen after perusing all of the websites. I have a trip booked on the Alta, and looks to be a sweet setup...combination of diving and pure pampering on the eating side. What could be better?