I've seen lots of people ask about the long Guayaquil layover upon landing from the Galapagos at approximately 3 pm and waiting for a connecting flight at 11 pm. Here's what I just experienced: contrary to some postings, the American Airlines check-in counter did not/not open until after 8:30 pm for the 11:35 pm flight to Miami. If you think you can check in your bags at 3 pm for your 11:35 pm flight, it just isn't possible.
However, also contrary to earlier postings, there IS baggage storage at the Guayaquil airport. It's located on the lower floor, the arrivals terminal. Thus, it would be quite simple to check your bags and do something in the city for a few hours before checking in for your late night flight.