First off it is still warm in Sept. & Oct. We were there at the BWV & WL during the week of Oct. 25th and it was tank top and shorts weather. (I being a floridian do not like the cold much.) The pools were definatly being utilized and I actually got sun burn on my arms from watching my little one swim in the kiddie pool. The crowds were very manageable. Not a very long wait at all for most rides.
Sept. I think is the ideal time to go. Although you will be smack dab in the middle of hurricane season, and I have four words for you...
Charley...Frances...Ivan...Jeanne!
Will, Florida experience four hurricanes again? Who knows, we do not even want to think about it!
You'll have to list the pros and cons then decide.
One thing about Oct. though is the Food and Wine festival at Epcot. (Loved it!)
Lot's of things to consider.
Good Luck!
Jaime