We usually spend one night in, and then two nights in Quito on the way out as well. After 10 days of adventure, most don't balk at the surprisingly inexpensive upgrade to the Hilton Colon. (use points!) It is situated next to a huge park that is an ongoing craft market. The city itself isn't a complete "no-go", but I counsel my groups to stay in that park and the surrounding street. Go to tourist sites in guided groups, during mid-day. It can get pretty icky and fast. For this same reason, I send no one out of harbor hotels and into Belize City (as in your original post) or the other common gateway in Ecuador, Guayaquil.
You're embarking on an adventure that few North Americans have ever enjoyed. We are absolutely brainwashed by the advertisers in "dive magazines" and they only represent the liveaboards. It's interesting that Brits and Europeans treat the Galloping Pogos as a backpack or day-dive op destination. They start their journey from the 0° Meridian, so for then, the G is on the dark side of the Moon, comparatively. It is to them what the Maldives is to us in the States... a really long trip!
The Island Hopping is a great way to save serious money and see a lot more of what the Galapagos really has to offer. I like schooling Hammerheads and Mobula Rays, I like to watch the Seals- but there is so much more to see. The local guides are so enured to Hammerheaded-itis that is all most of them bother to show you. There are two distinct Nudibranchs that spend their entire existence trying to kill the other species.
The lava tube tours (Sta. Cruz), the both of them, are not to be missed. If you only have time for one, go for the one run by Oswaldo- he was a photographer (back in the day) along for the "trip" with Ken Keysey and Janis Joplin on the Magic Bus. That is no joke.
Likely you will meet the guy who established all of the new far-flung land based dive ops, he is a Naturalist Guia (guide) from the C Darwin Research Station and was featured in Al Giddings Galapagos IMAX-3D... his name is Mathias Espinosa. He owns ScubaIguana on Santa Cruz, just outside of Darwin Station- which I (and many others would) suggest that you charter with.
Please write a detailed report and let others know that there is more than one way to dive the Galloping Pogos.