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.
Prior to checking in for the flight, you must go through two steps: first, obtain a Control Visitor Card (or TCT). You'll need to present your passport and $10 at the "Consejo de Gobierno de Galapagos" counter. In Guayaquil, this was at a window just to the left of the Aerogal check-in (at the new Quito airport, it is near the "A" check-in counters and next to where you can buy air tickets for the domestic airlines). Second, you must have your luggage inspected by AGROCALIDAD, which in both airports is right next to where you get the TCT. They will place a nylon zip tie onto your luggage, and then you can head to check in for your flight. Our flight was on time, and we arrived in Baltra at 9:20am (Galapagos time). Upon arrival, you will show your passport and the completed TCT. You'll get back the bottom portion of the TCT which has to be shown when you depart the Galapagos. Celebrity includes the entrance fee to the national park in the cruise fare, so your name should be on a list of those who have already paid. The check-in materials included a voucher that we were supposed to present, but the agent in the Galapagos just found our name on the list. You should not have to pay $100 at this point, but if you do (as another couple on our cruise who traveled alone did), save your receipt and Celebrity will reimburse you onboard the Xpedition.
We arrived approximately 90 minutes before the Celebrity charter flight and were expected to just hang out at the airport until everybody else arrived. Crew members (naturalists) were already waiting with signs and took our check-in luggage at this point for transfer to the ship. We did some shopping and reading, but another group traveling alone that arrived early hung out in the VIP lounge. At around 11am (Galapagos time--ship stays on mainland Ecuador time), the 90+ people on the charter flight arrived and we headed onto buses to transfer to the panga for transfer to the Xpedition.
The trip (itinerary A) was awesome, with Monday's two visits to Espanola, the deep snorkels and panga ride at Punta Vicente Roca as our favorite moments. Our wet landings were all in sandy areas, so my travel companion who did not have water shoes had no problem just going barefoot, drying his feet with putting on his shoes once on land.
On the final day, we left the ship at 8:30am (Galapagos time) and were on a 10:45am flight. The Xpedition help desk told us any flight after 10:30am was okay to book, and we were in the waiting area easily an hour prior to our flight. The Celebrity charter flight was scheduled to leave at 11:20am and arrived in Quito about 30 minutes before our flight, since we had to stop in Guayaquil.
Having successfully done just the seven day option, I was happy to have everything work out so well. Of course, by booking on your own you run the risk of getting flight delays and missing the cruise, so the other options Celebrity provides that include the charter flight definitely gives more security. I just wanted to include my experience so others that cannot or do not want to do the longer options have some help. Finally, we were two of nine thirty-somethings on our cruise (there was also one child), but the crowd definitely skews older. Still, we had a great time meeting all sorts of different people of all ages who all seemed to have an adventurous spirit. We would definitely recommend the experience to anybody who is considering it!