I would definatley give Quito more time if you have it. Quito is a fascinating city both history and culture wise once you start digging in to it. If you are only going to give it one day I would suggest that you hire a car and driver.
I spent a month in Ecuador in '92. The Quitenos I met were very proud of their city and took me to places that I never would have found on my own.
The Galapagos are by far one of the most unique places on this planet, truly a once in a life time trip. My one bit of advice for anyone considering a Galapagos trip would be to do it on the SMALLEST boat you can find. Keep in mind that all of the islands you are visiting have virtually no facilities, docks etc. and you will be going ashore in small boats landing on beaches more often than not packed with lounging sea lions. The Galapagos Legend looks like 300' of mighty fine ship but the thought of queing up with 100 other cruise passengers to go ashore and visit the wildlife sounds like a bit much (at least to me). I'm surprised that the Ecuadorian government is allowing ships that size in.
I was with a group of 5 and we chartered a 40' local boat out of Puerto Ayora. The charter included a Capt., cook, crewman and the required naturalist from the Darwin Institute. Being on a small boat allowed us to pretty much set our own schedule. We were able to catch our own fish and lobster. The highlight of being on a small boat for me was the opportunity to get up every morning, jump off of the back of the boat with a mask and snorkel and play "tag" with the sea lions.
An unforgettable experience anyway you do it !!