While the vast majority of tourists stay either on boats or ships, or at one of the hotels on either Santa Cruz or San Cristóbal islands, it is possible to stay on the much-less developed islands of Isabela or Floreana. Staying at either of these will definitely give you the sense of being off the beaten path, while still allowing you access to all the same types of tour and activity options available to those who choose a more traditional route.
You can get to Isabela from either Santa Cruz or San Cristóbal on a commuter flight with EMETEBE airlines (tel. 05/2526-177; emetebe@ecu.net.ec), or via a boat ride from Puerto Ayora. Isla Floreana can only be reached by boat, and it's a slightly shorter ride to Floreana from Santa Cruz than from San Cristóbal. If you plan to stay on either one of these islands, you should probably reserve your room and arrange transportation in advance.