We went this last September (10-21), and enjoyed it. The crowds were amazingly light, even the biggest attractions were walkons most of the time. The only time we had to resort to using FP was Saturday at MK, and I think that goes for any Saturday at MK, any time of the year you go.
Even though we are from Nashville and are used to heat, it was pretty dang hot and humid. There was also thunderstorms/rain almost every day, but that didn't bother us. We popped our ponchos on, opened up the umbrellas, and had a great time!
IMHO, one of the major disadvantages of touring in September are the reduced park hours. Granted, with everything essentially being a walk on, you don't need 14 hours to tour a park, but there is something so magical about being in the parks at night. Plus, there are reduced firework/parade schedules and that can sort of stink, too.
The other major disadvantage to touring in September is the amount of rehabs going on. Don't get me wrong, I am thrilled that Disney is performing needed rehabs, it's just that if this is your once in a lifetime, see as much as possible trip, you may be slightly disappointed. While we were there Haunted Mansion and Maelstrom were completely closed for rehabs, 5 countries in WS had partial rehabs going on, Impressions de France was running on a reduced schedule, and (of course) Carousel of Progress and Timekeeper were closed.
Overall though, I would definitely recommend September---just make sure you go after Labor Day!