Wazzo-
We were originally scheduled for the YC Gazebo but changed to the Wedding Pavillion later on - and weather was one of our reasons why.
The backup location for the gazebo is a conference room at the Yacht Club. They will move you there only if it is raining too hard to have any sort of ceremony outside - if it is misty, they'll keep you outside so you can have your location.
I was afraid of being in a conference room (we were there one year ahead of our date and it rained the whole time, which made me nervous) beacuse I felt like we could have had that look at home and it wouldn't have been "Disney" enough for our guests to have made the trip.
I am WAY too much of a control freak, though, to have an outdoor location, so please do not take this as any kind of advice for you.
I think that deep down, every bride knows what she can or can't handle in terms of being flexible, so it's best to make your decision based on what you want.
As far as times, when we were booking the Gazebo was available on the odd hours up until 3pm (9am, 11am, 1pm, 3pm) but I think those times may have changed to the even hours, so it's best to check with an EM to be sure. I am fairly certain that only daytime weddings are permitted at that location.
Hope this helps!
Jennifer

Intimate Wedding 12/11/06
Wedding Pavillion/Commanders Terrace