Does anyone know of a tour to the Galapogos Islands that does NOT require you to fly into/out of Quito? Altitude sickness is a big problem for me.

All flights (or nearly all flights) to the Galapagos originate in Quito and stop in Guayaquil (about at sea level). Flights back to the mainland first stop in Guayaquil and continue on to Quito. Even if the tour itinerary talks about time spent in Quito, can you join the group in Guayaquil? I'd contact any of the tour operators you are looking at and ask.

I do like Guayaquil, but from a visitor's standpoint, it is nowhere as interesting as Quito.

(Sorry for the delay in responding...out of town and out of touch!)
thanks for your input. Looks like I'll have to do some research on travel from the US to Guayaquil.

On my trip with Lindblad Travel we stopped in Guayaquil outgoing and had a choice of Guayaquil or Quito coming back...so there is no reason to stop in Quito

It's almost as easy to get to Guayaquil (airport code = GYE) as it is to Quito. American and LAN fly from Miami. Continental flies from Houston. GYE is a beautiful new airport and is very easy to navigate. You'd likely have to overnight the night you arrive and the night before you fly back to the U.S., but that would be the case with using Quito too. GYE is about a 15-minute taxi ride from the center of the city, where you'll find a good selection of hotels. There are other hotels closer to the airport too.

Delta will begin flying from Atlanta to Guayaquil in December too. That's one more option.