We had an excellent experience in the Galapagos on Celebrity Xpedition. Other people have detailed the itineraries and ship in great detail, and the ongoing discussion in the Role Call is quite helpful. The vast majority of people do the 10- or 11-night package that includes time in Quito and a charter flight to and from Baltra. Unfortunately, my work schedule prohibited us from arriving in Ecuador until Saturday, so we booked the 7-night package only. Having completed the experience, here are some helpful hints for those trying to get to Baltra on their own.
Booking flights: currently there are five non-charter flights to Baltra every Sunday--two with Aerogal, two with TAME and one on LAN. All originate in Quito, stopover in Guayaquil and then head to Baltra. LAN has the most user-friendly website, and it's easy to price and book flights, but the flight lands in Baltra just before noon (Galapagos time), which seemed too late. That left Aerogal and TAME as better options. I did some research on TAME, and while you can price and find availability on their website, you cannot book with a US credit card. I did find that by calling their Miami number you could secure a reservation and then pay either by bank transfer or credit card (for an additional fee). Aerogal's website did not show any availability on the date we wanted to travel. However, we were also booking an excursion to the Amazon region of Ecuador (Napo WIldlife Center, also highly recommended), and their booking office (and probably any Ecuadorean-based travel agent) was able to secure seats for us within 24 hours of my request. We decided to book with Aerogal because their flight was scheduled to arrive the earliest.
We flew from California to Guayaquil through Panama City and arrived at just after noon on Saturday. Guayaquil isn't that exciting, but we were happy to have an afternoon to explore the Malecón and Las Peñas. We stayed at the brand new Holiday Inn which is less than a 5 minute walk from the airport (they also have a shuttle). On Sunday morning, we walked back to the airport to start our flight.