I've gone in September 3 of the past 4 years. It is still pretty hot (bring a misterfan if you have one), and you stand a good chance of a thundershower each day. But rest assured, they are fast, rarely lasting more than an hour. As for crowds, the parks always feel crowded, but the lines for most attractions are fairly short. There are exceptions, like Soarin and Toy Story, but clever use of fast passes and help those. The biggest challenge is ADR's. September has been free dining month for the past 4-5 years. This means Disney resorts are filled, and all the restaurants get booked quick. If you don't have ADR's yet, make them ASAP.
I've really enjoyed my Sept. trips. The MK is decked out for Halloween, and since I stay at the CR, i get too see HallowWishes from the resort. You should have a great time