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Many exist. But your cruise captain has little sway. The Galapagos National Park Service proscribes and enforces all itineraries. This includes the visitor sites and the hours of the day you can be there. The assignment system helps prevent overcrowding the wildlife and environment.
If you have a strong preference for visiting a particular island or visitor site, be sure to select a cruise that satisfies your desire.
Typical cruise lengths vary in the Galapagos Islands from 4 days (3 nights) to a couple of weeks. With the first, you will miss some important shore excursion sites. And the second is too long for most travelers. For most visitors, a length of 8 days (7 nights) is ideal.
If you desire an 8-day (7-night) cruise, I strongly recommend that you don’t book one that also sells half-week cruises. Such boats cannot travel to more distant islands because they have to return to their home port in the middle of their sailing week to disembark the half-week passengers and embark their replacements.
Some travelers book hotels in the Galapagos towns Puerto Ayora and Puerto Baquerizo and take daytrips to nearby visitor sites. The drawback is you stay only in hotels and miss the joy of cruising on a sleep-aboard ship or yacht. And, although you visit nearby islands, you miss more distant islands, some of which are musts.
Tourists are allowed to visit only a very small fraction of the Galapagos National Park. The rest is off limits. However, the allowable areas rank high in interest.
The daily schedule is more or less the same for nearly every 8-day (7-night) cruise ship and yacht. Participation in each activity is optional (except for evening briefings and the one-time lifeboat drill).
It's a challenging schedule. But for most visitors, this will be their first and last time in the Galapagos Islands. So maximize your Galapagos experience to the best of your physical abilities while you're here.

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