I was in South America for 6 months and lugged around a big Tunra case with a large Canon EOS outfit. That was before I moved up in format. I think medium format (Pentax 67 with 45/90/165 mm) and my Canon 35 mm with some type of zoom and a 400 5.6 would be ideal. It is a hard choice. Take the largest format that you can manage, ideally in something like a Tundra case which is waterproof and dustproof. I also took a Bogen monopod which is cheap and makes a good walking stick/weapon while wandering the streets and fending off stray dogs.
You must stay with the naturalist but not hip-to-hip. You can wander up the trails. They are pretty good about not letting people trample the place off trail or get offensively close to wildlife but I suppose there could be variability. I was with a small group. I did not feel limited by the group.
For shoes in the Galapagos, I would take Keen sandals. Think about packing your own snorkel if you are fussy about fit, etc. I would get a fairly cheap one here and just leave it behind.
If you have time, go to the Eastern part of Ecuador. I never find the tropics to be very photogenic. Too damn hot for me. But the birdwatching and the experience is worth it. A lodge called La Selva is very nice. It is cheaper (a little) if you set it up in Quito. If you go to the buggy parts, I recommend:
It packs up very small and light and greatly improves sleep.
I don't know if it is still there, but the South American Explorers Club in Quito was a safe place to leave pieces of luggage while moving from one climate to another.
Make sure you have the Lonely Planet for Ecuador: