Even with all the research and reading, it's difficult to know of good places to go until we talk to the locals and they give us recommendations. We probably won't make it to these places in Ecuador on this trip, but next time:
1. One itinerary option from Quito: head southeast on E45 through Tena to the sleepy jungle town of Misahuallí, spend a few nights exploring the edges of the Amazon, then make way towards Baños de Agua Santa.
2. For a more coastal experience, it looks like the best place to fly in to is the big southern Ecuador city of Guayaquil. From here, Salinas beach has been recommended, as well as "poor man's Galapagos" at Isla de la Plata.