Sept is one of the least rainy times. But in the dry season there can be garua, a misty fog. Pleasant temps, one of the coolest times. Seas can be a little rough that time of year.

weather chart
http://www.fodors.com/community/south-america/four-days-in-galapagos.cfm

Don't know about Red Mangrove.

Galapagos Islands trips to the uninhabited islands are done in groups and there are strict rules on such things as the guide to visitor ratio, staying on the paths, visiting islands on a set schedule, etc. All for the protection of this unique environment. Even if you do land-based trips, your access to islands with sensitive habitat will likely be with a group. For a price any excursion or an entire boat can be made into a private trip, but it could be very expensive.

Sea sickness--Nobody is worse than me. I can't do merry-go-rounds or Imax. I even get carsickness if the roads are winding. But over the counter Bonine works great. I've been on numerous rough seas, including Galapagos in mid-August when the seas are rough, but have no problem with Bonine. It never has failed me.

Concerns on being part of a tour--The focus is on the wildlife on shore and not the other people. It is always nice to enjoy the other travelers, but you can focus on the two of you, the guide's info, and the islands you came to see. On the boat you can wear headphones to shut out whatever you wish to shut out if needed. The two Galapagos trips I did had mostly great people. The destination attracts a certain type, especially on the smaller boats. I continued conact with 3 of the people I met aboard our 16 passenger boat and I couldn't stand 2 people on one of the trips and easily avoided them.

Good luck with your South American trip.

If your concern is about seasickness and being stuck with people we don't enjoy. You might be interested in doing a land-based holiday in the Galapagos. Briefly, you're staying in different islands and can manage your own activities as walk, kayak, snorkel and cycle! Spend also your time in the small towns of the islands allowing you to eat out in restaurants, wander along the sandy beaches and have a swim as the mood takes you.

In September, the air temperature reaches its lowest levels (19C-66F). Galapagos Penguins active around Bartolomé. Snorkelers can swim with penguins active at the surface or torpedo-like while underwater. Sea lions are very active. Females have reached estrus stage, and so harem-gathering males are constantly barking and fighting. Shore fighting is common. Most intense sea lion activity on western and central islands. Most species of sea birds remain quite active at their nesting sites.