I had lots of similar questions! Here are my thoughts:
1. Most of our days were warm and sunny and it generally stayed warm at night, but we typically spent the evenings in the dining room rather than outside (except for 2 nights when we went to the top deck to stargaze). I had a light hoodie I usually wore but definitely didn't need anything warmer. Quito was pretty warm as well, but we just had the one day there so it might vary. We traveled from northern California in our usual fleece jackets, but we didn't use them again until we flew home. The water was a little chilly, but fine with the wetsuits.
2. Yes, and you can choose short or long sleeved, or even full body. We were fine with the shortie option. You'll get fitted for them on the first morning along with your mask and fins and then it will be ready on the deck for you each snorkeling trip.
3. There was no space under the bed, but there was a closet as well as several drawers. I was able to put my carry on rollerboard under the desk/vanity area, but I'm not sure where something larger would go.
4. We saw penguins (including in the water with us) but not flamingos. The birds were amazing though, especially on Genovesa Island the last day.
5. We arrived on our own, but we flew to Baltra a day early and stayed on Santa Cruz for a night because we didn't want to risk missing the departure if we had flight delays. We actually did have some issues leaving Quito because we were confused about getting our tourist transit cards and getting luggage screened, but we ended up making our flight just fine. The other solo travelers did the same thing. Once back at Baltra, the Celebrity reps were there and they reimbursed us for the cost of the transit card and park entrance fee (it's included in the Celebrity pricing, but they can't pay it for you if you aren't on the pre-cruise tour). They got us back to the airport as well.
6. We were fine with trail sneakers instead of full hiking boots. I used Keen water sandals on wet landings, but I used sneakers for all the dry ones. We otherwise just wore long sleeve hiking shirts or rashboards and long hiking pants everyday, as well as our sun hats. I brought shorts and short-sleeve tops, but I only wore those on the boat when I could be in the shade. I was also happy to have 2 swimsuits because we usually had 2 snorkeling activities per day and I hate getting into wet swimsuits. I brought a clothing line with clips to dry clothes each night, but it was tricky to find a place to hang it.
7. I'm sure you will have a fantastic time!