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Need a lot of help with first trip to Ecuador!

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I am in early stages of planning my trip to Ecuador and Galapagos for next year. And as always, none of my trip goes without Fodorites advice.
1. I am trying to figure out when to go. We would like to visit both Galapagos and Amazon, so I am looking for a better weather for both, and that sea is not too rough. It does not seem like the same season works well for both. Will March be OK? Seems like OK for Galapagos, but too wet for Amazon. Looking for your advice.
2. I am thinking of 5 days for Galapagos on larger ship (like Explorer or Legend) to minimize sea seakness risk. Any other suggestions for a ship?
3. And I am thinking about 4-5 days in Amazon. Any recommendation for a Lodge? Sasha looks good, but seems like a long time to get there. Any other recommendations?
4. I also would like to visit Quito, Otovalo, possibly hot springs, and probably that’s it, because I cannot vacation for more than two weeks. Are there any suggestions of logistics – what to do first, and what to do last?
I appreciate your help and thank you in advance!

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