This is a decision generally based on time and price. Boats are constantly working on heavily regulated 15day cycles designed to ensure that the quotas for visitors per islands are not exceeded. Vessels pass Santa Cruz and Saint Cristobel (both of which you can fly to) on various points during this cycle and it is possible to jump on and off at these points. For most people 8 days is a good compromise of time and money.
Your two basic 8 day trips, starting and ending in Santa Cruz are as follows.
- A week covering the east, north and south islands. My recommendation.
Of the 4 most unique and recommended islands this should cover Floreanna, Espanola, and Genovesa. Both Espanola and Genovesa are inaccessible by day trips and offer incredible biological splendour and diversity on the land. They are also the breeding grounds for waved albatross and red footed boobies respectively. Whilst the snorkelling with the sea lions of Floreanna is magnificent. You also visit Saint Cristobel and Kicker Rock, which, with good visibility, offers the best snorkelling the Galapagos has to offer.
- A week around Isabella and Fernandina
Isabella is a huge island with an active volcano, it offers some great snorkelling and a days good hiking, which if the weather stays clear can give you some great views. The cruise will take you west of this island to Fernadinha, also inaccessible by day trip. Here is your only opportunity to see the endemic, flightless cormorant. On top of this, this area around Isabella and Fernadinha is where 80% of the Galapagos penguins can be found and therefore offers you the best chance of sightings.. However there are small populations around Bartolome and Floreana and Pinzon.
As touched upon earlier, it is possible to join at slightly different points of the cruise for different periods of time. My recommendation would be to pick the itinerary that allows you to visit the most of the following: Genovesa, Floreanna, Fernandinha, Espanola and Kicker Rock.