We started to write this section, and then found the website below which has much of what we wanted to say. It reinforces the idea that those on a budget could have quite a full Galapagos experience by staying in hotels or hostels on the islands accessible by high speed ferry, and taking day trips. A good Galapagos natural history book would help fill the gaps you might experience because you don´t have a top notch guide. Cruise boats are wonderful, and you see more islands, but they can be more expensive than other options.
Some things it doesn´t say follow.
Cruise boats seem to start at about $250 per person per day. To travel in the park you must have a guide. There are about 120 prescribed tourist sites. Guides will only take you to those sites, as they would lose their license for doing otherwise, and might lose it if you go anywhere else.
Acceptable hotels with air conditioning, wifi, and hot water are available for about $70 for a double room. Double rooms in hostels are available for $50-$60 per night. Of course, you can spend more and get more luxury if you want. High speed ferries between the islands cost about $30 per person each way. Day trips seem to cost $100 or less per person for an average of perhaps $40 per person pre day.
So you may see a little more, and have a better guide, on a cruise boat, but you could have a wonderful Galapagos experience without taking a cruise by visiting some of the islands for several days and others by taking a day day trip to one island. .
Cruise boats sell their unfilled cabins at a discounted rate, particularly during the off seasons. The discount becomes more and more substantial as the departure date approaches. Evidently 50% is not unusual. So another alternative is to arrange your plans so you have time to take a last minute cruise at a discount. You won’t find these discounts during the Christmas, Easter, or North American summer months.
All visitors pay a $100 fee to enter the Galapagos plus a $10 Galapagos visa fee. Visitors are permitted to stay for 90 days. Ecuador also has a 90 day requirement which says that visitors may only stay in Ecuador for 90 out of each 365 days, although with money and lots of paperwork you can apply for more time. All flights to the Galapagos are to and from Guayaquil. There are cargo ships going to the Galapagos but traveling on these has no advantage relative to flying.