Thanks again to Roatanman for a well-informed and well-balanced posting. I just got back from 1 week land-based diving out of Puerto Ayora. The liveaboards and land-based diving boats are only allowed to dive (no landings) and the cruise ships have specific permits for specific islands on specific days. However, the main island Santa Cruz has such a lot of great stuff to see (giant tortoises in their natural environment [not the Charles Darwin centre], blue footed boobies, blue herons, tonnes of iguanas). I would seriously recommend spending at least a day, and walking to Turtle Bay (beautiful beach with lots of wildlife).
As for the diving, the current is very strong (especially at Gordon Rocks), the visibility poor and it is tough getting into a boat in 6ft swell. But in terms of the amount of wildlife we saw from just land-based trips (pretty much everything except the whale shark), it more than justified the trip to Galapagos (and was much cheaper than a liveaboard). We went with ScubaIguana, who were very professional and friendly. But from what I understand, when the conditions are better (warmer, less current, better visibility), there's much less wildlife.
Enjoy your trip whatever you decide!