... the Galapagos - another not cheap possibility.
This is a common misconception. There are flights from Guayaquil to Baltra and from Puerto Baquerizo Moreno back to Guayaquil with at least two airlines and Lan (now Latem) has a deal where you can get cheap internal flights in South America if you buy your intercontinental flights with Lan. Once in the Galapagos, a fully catered cruise around the islands is the more expensive option (although you can get deals on them too) but it is possible to use the inter-island ferries to island hop and stay in cheaper hostels on the islands.
The islands are well worth visiting and, if you are in Ecuador and have the time, they really are a 'must visit' destination.