My wife and I are planning to go to Peru and Ecuador. And also would like to visit Galapagos while we are there so I have quite a few questions but will start with 2:
Endpoint in either case is the US.
It depends!
I am sure you can travel in a way that is super interesting and not too stressful for you son. This would mean flying the long distances between southern Peru and Ecuador, staying in nice hotels and don't travel too far overland every day in a rental car. But of course, all that has it's price.
If you want to use public transport and stay in cheap hotels it becomes a bit more stressful. I never traveled at night, but there are still some long bus rides during the days.
I am sure the animals on Galapagos would be very interesting for a six year old. Inca ruins maybe less so.
I think the weather in Ecuador is similar most of the year, but in the South of Peru it is much colder in the winter. So depending on when you go, you may want to go to Peru in the period that is closer to summer (our winter). On the other hand, Machu Picchu is less busy in the low season and the Inca trail is closed in February.
I am a native from Ecuador. I have been in the Galapagos with my nieces and nephews and I think it will be a great experience for kids (6 and up) if they are young explorers that want to have fun while having activities with an educational approach.
Young kids could learn about endangered animals and habitats, and about Darwin and his theory of evolution. The activities start really early in the morning so be sure the kids have had a good rest the night before.
For the route I would first visit the Islands and then Peru.
I have recently visited the Galapagos with family having 3 kids, they enjoyed a lot there and Specially Galapagos is the best place to visit. There are no such problems we faced during our tour because of children, as we have already booked out the tour and they include all the important amenities required for small children. Our overall trip was awesome.
