Without question a cruise is still the most recommended way to visit the Galapagos Islands. Simply because you are able to visit the islands that are located further away, which gives you a better opportunity to see a wider variety of wildlife and landscapes.
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The main difference and a definitely surplus of these tours is that you can combine your stay in multiple hotels each based on a different Island.
For that reason you lose less valuable time traveling back and forward to the main island and are able to see sometimes different sites than in the hotel packages.