We've spent two weeks in September this year, and also a week in September two years ago.
The heat? Well....It's hot. And of course, we picked the hottest days of our trip to go to AK, which seems to have the least access to AC! Just be prepared to take it slow, visit the water parks and pools, and duck in and out of air conditioning to get refreshed. You'll be fine. It was entirely bearable.
The crowds were much larger in '07 than in '05 by our estimation, but the lines were never a problem. I can't remember the number of times we literally walked right onto major attractions, particularly at MK (All 3 Mountains were quick and easy for us. But I agree with a previous poster when they said that there were more people walking around. Bus service to CSR was incredibly efficient and quick, as it always seems to be for us at any time of year. The previous September trip was to ASMo, and the bus service was mediocre at best, with very long waits at night getting "home" from the Parks.
ADR's were trickier to come by this time around. We tried and tried to get into LeCellier, but never had any luck. We did manage to get Coral Reef, Ohana and a few others at prime dinner hours, though, so it was hit or miss. As always, just try and make the ADR's as soon as you can.
Free Dining makes September a no-brainer for us, and the kids don't seem to mind missing a bit of school, either (and fortunately for us, the school doesn't mind)!!