Most of the things that are issues with going in September have been covered, I just thought I would mention a couple of things that I've noticed that might give indications regarding crowds.
We are booked for this Sept. (5-11) with the Free Dining. About three weeks ago, once all our travel plans were finalized, I called WDW-DINE to make our ADR's for the trip. Some of the places are relatively popular restaurants, and a few are character dining - the ones that are often harder to get ressies for and where they are serious about calling 180 days in advance.
When I called, it was about 90 days in advance of our trip. When talking to the CM, mentioning the restaurant and date and for what meal, I asked "what do you have available" - her reply - "what time do you want, it's wide open."
While I know that many people don't make ADR's - considering the Free Dining Promo, the wide open availability for some of the most popular restuarants (ones like Le Cellier, Coral Reef, Chef Mickeys, Cindy's, etc.) makes me hopeful that crowds will be low.
It's been a while since I have been at Disney, last trip was in '98 with my wife - before we had kids. We were there in September when Hurricane Georges went through. It really only gave us one bad day of weather. That was easily offset by the virtual lack of lines on some of the popular rides (we walked onto Pirates for example - and even with AK just opening, we only waited about 15 minutes to get on to the Kilimanjaro Safari).
Yeah, it was hot - and we're expecting heat for this trip. For us, the low crowds make it worth the heat and chance of hurricane.