How does this Ecuador Itinerary Look?

Definitely stay at the airport if you are going out the next morning. We liked Quito Airport Suites, owned by an American named Dom. He actually has two locations, both within 10 minutes of the airport.

We really liked Quito and saw only the old center. Three nights was enough there. But we had 2.5 weeks, including the Galapagos, 4 nights in Chugchilan, and 2 nights in Cotopaxi (very clear one day--amazing).

Have to leave Cuenca for next time. The #1 most important rule of travel is: always assume you will be coming back to a place. Well, after the actual #1 rule, which is; never pass a bathroom/toilet without using it, whether you have to or not.

I have to agree with those who say the itinerary is too full. One possibility is to choose either Cuenca or Quito to visit. The bus form Latacunga to Quito is only a couple of hours. Latacunga to Cuenca is 6+ hours. And yes, you have to add extra time getting to and from stations and hotels. How do you plan to get around The Quilatoa area? If planning on buses, you need more time, as they are inconvenient and not frequent. If you are planning to use the private transport offered by hostels and lodges, it's easier but much more expensive. Worth it, in my opinion, for a short trip. But it needs to be arranged in advance.

The Andes villages around Quilatoa are still fairly remote, in spite of new roads, and travel is slow. That is the main difficulty of your plan.

I agree it is a good idea to stay near the airport if coming and going from Quito in quick succession. Hosteria San Carlos is a good place. The trip in or out of Quito proper can take 2 hours, turning a half day of travel into most of a day.

It's also worth noting that acclimatizing to altitudes will slow you down somewhat if you plan to be active. The first couple days you will not be feeling as well as usual.

You know, generally I totally disagree with the notion that "you'll always be back" but in this particular case it kinda makes sense--because I absolutely intend to go to the Galapagos at some point in time. That clarifies things because it means I can save Quito for a later trip.

So, maybe I'll just work my way down to Cuenca and take the evening flight from there the night before I leave back to Quito.