If doing the Galapagos again in the future, I’d recommend the following:

Definitely book a cruise. 5 nights is probably the right number for me before I go stir crazy. I highly recommend the Nemo III as we all agreed it was the best, most comfortable boat out there (much of it due to the extra width of the catamaran). Ideally the cruise leaves straight from Baltra after landing at its airport. That way you can avoid hitting Santa Cruz more than once as the cruise will most likely stop at Puerto Ayora to see the giant tortoises & Charles Darwin Research Center. With the exception of one cool street that transforms from nothing during the day to a thriving cheap fresh seafood scene at night as tables & chairs crowd the street, we found Puerto Ayora to be stifling hot & offering little more than shopping, a shitload of tourists (relatively speaking bc it’s still a little city with less than 10k population) & day trips from the main port. Hopefully with the cruise, you can knock out some far off islands that are not accessible by Santa Cruz daytrips. Few cruises include Genovesa & that was important to us & turns out we had one of the most incredible snorkeling experiences ever in Darwin Bay. 

Definitely visit Isabela. Even if you’re lucky enough to visit Isabela & Fernandina on the cruise, head back to Isabela to stay on the island. It’s an easy 2hr boat ride from Puerto Ayora & worth it. 

Consider flying out of the airport in San Cristobal, accessible via boat from Puerto Ayora as well. Or stay in Puerto Ayora if you want to knock out other day trips. Gina & I spent a couple days here before the cruise & enjoyed the hike to Tortuga Bay on day 1 where we saw a gorgeous beach, a bunch of marine iguanas & swam with our first sea lion & marine iguana as well as a day trip to Santa Fe Island where we saw our first blue footed boobies, I realized birds were really cool too, we snorkeled with sea lions & watched jumping manta rays. I certainly don’t mean to be negative about Puerto Ayora; rather, my preference is overwhelmingly in favor of Isabela. 

I inexplicably caught a head cold in the Galapagos so unfortunately was unable to dive. While disappointed at first, I then saw such incredible marine life snorkeling (& freediving) that I felt as if I wasn’t missing out too much. However, next time I will dive. And the best dive trips are run out of Puerto Ayora as well as one out of San Cristobal. 
The Galapagos isn’t for everyone. And it’s expensive so it eliminates most of the backpacking crowd. You need to be really into exploring nature & marine, bird & wildlife in an environment that’s been highly protected & regulated since the 1960s. Due to the regulations, a naturalist guide is required to do just about everything on the islands. Two exceptions are the hike to Tortuga Bay in Puerto Ayora & the amazing snorkeling on Isabela in Concha de Perla. As a result of these protections, the wildlife doesn’t seem to feel threatened & are oftentimes quite curious & playful. It made us wonder how much better the world would be if everywhere had the same common sense environmental protections. I found it to be absolutely amazing & this is one place where I know I’ll return within 5 years.