We just went this past September, and I do have some things that made September rough:
1. The parks weren't all that busy BUT because they weren't a lot of the Fast Pass terminals weren't open. However much I didn't "need" the fast pass with short lines, it would have helped tremendously with two small kids to have a set time to come back to the more popular rides!
2. I think they limp some of the rides along until Labor Day and then close them for "refurbishments". We missed out on a lot of rides that were being worked on. My DD was unhappy that the rocking roll roller coaster was closed.
3. The busses were INCREDIBLY slow. It is probably because they cut back on the number of busses when the numbers in the parks go down. We actually missed our Magical Express shuttle because it took us an hour and a half to get back to our resort from Down Town Disney.
4.
Free dining does PACK the restaurants. We had advance dining reservations and still waited 30+ minutes for every seating, and it took a long time at each meal since the restaurants were full to capacity (and then some).
5. It is hurricane season, so buy the insurance! And rain is very common. We missed a few parades because it was raining. We got thoroughly SOAKED a few times too.
6. It is REALLY REALLY REALLY hot! I had no idea how much heat just saps you of your will to move!!! I can't count the number of times I would have paid to just lay down!
I went in May in 99 and if I am going to pull the kids out of school anyway like I did this September, I think we will opt for May next time!