Since we've got back, I've looked at a number of Galapagos trip offerings from various companies. There is a huge range of content, and I'll make some comments later on what to look for in a trip. But... first look at a video I put together that is just a series of images from the trip, set to music. Watch it and then decide whether to read further:
Galapagos 2014 - two weeks on the Mary Anne
Almost the entire Galapagos Islands are in the National Park, and tourism is strictly controlled to avoid damaging the resource. Each ship must have a local guide. The islands are currently divided into some 70 different visitor zones. Access to the zones are limited by time of day and number of visitors. Every tour vessel or private ship must have a permit for a specific time and day for each zone it visits. We never saw more than two other vessels at a site. Itineraries are sometimes changed at the last minute because they couldn't get a permit for the exact time and day they wanted.
Most flights are into Baltra, which is roughly in the center of the islands. From Baltra some tours do the Eastern Islands, some the Western, and some both. On our tour we lived on the boat, but there are many hotels, and some tours operate out of the hotels with day trips.
Our trip covered both the Western and Eastern Islands and we lived on the Mary Anne, a three masted barkentine. Almost every day we had short (a mile or two?) walks on the islands, snorkeling, sometimes sea kayaking, sometimes zodiac trips around the edge of the islands. I found the Eastern Islands a little more interesting if I had to choose, but some favorite moments were in the Western Islands.
Things to look for in a tour:
First, look at days on the mainland (Ecuador) vs days in the Galapagos. I've seen some with three mainland days and four Galapagos days. Get as many Galapagos days as you can. Ecuador is fine, but ordinary South America travel. Galapagos is unique. We had two mainland days, 15 Galapagos days. The current REI tour has eight days, all in the Western Islands except for the mainland airport time at Guayaquil.
Second, if you only have a week, do the Eastern Islands, and be sure the tour includes Tower (Genovesa) Island. I don't see how a hotel based tour would have time to get out to the remote islands, but don't know for sure.
Third, it is mandatory that your trip include lots of snorkeling opportunities and land hikes. One of the most impressive things is the sheer biomass of the fish in the sea. Sometimes the clarity is not great, but the numbers of fish are staggering. The occasional large shark is a sobering sight. If you cannot snorkel or hike, the zodiac cruises around the islands still allow you to see a great deal.
Museum of Anthropology , right along the edge of the waterfront. Go in and straight to the back where the oldest objects are. Some magnificent pottery whistles for example.
At the end of the trip we made our own arrangements and flew to Quito and then went directly to Otavalo to the Ali Shungu lodge. This is an incredible place to stay, and will get a separate post in a day or two. After several days there, we went to Quito for two days and then flew home.
Doing Quito last was a bad idea. Going to Otavalo and Ali Shungu is an excellent way to decompress from the Galapagos experience, but Quito was a traumatic culture shock. It is a huge, busy city. Worth visiting, but do it BEFORE going to the Galapagos.