Thanks everyone for the suggestion. If I spend 6 days total between Cuzco, Puno, Lake Titicaca. What would be a best place to flight back to Lima?
I don't want to go back to Cuzco to take the flight.

Day 1 - Lima
Day 2 - Cuzco, over night at Aguas Calientes?
Day 3/4 - Early morning train to Macchu Picchu, return to Cuzco
Day 5/6 - Bus to Puno, Lake Titicaca
Day 7 - Flight back to Lima, what is my option to take the flight?
Day 8/9/10/11/12/13/14 - Ecuador and Galapagos Island

Which city is easy and closer on Ecuador to Galapagos Island? Is Quito better option?
I don't want to take the cruise on Galapagos Island, it is very expensive. There are 3 people on this trip.
Is there other option on see the Galapagos Island without join the cruise line?