September was great - a lot of time the Fast Pass machines were turned off, there was literally no need for them. My son must have ridden Space Mountain 6-7 times, just hopping off, walking through the ropes, and getting right back on again! It was really amazing...
But other days, it seems like everyone got the memo about one park, and it was mobbed. The one day we spent at Animal Kingdom was crowded, and because they'd turned off the Fast Pass machines at some rides (Kali and Everest) there was no getting around lonnnnnng lines on those rides. I try my best to avoid the EMH parks on their given days - - it just draws the crowds, but this day at AK was not an EMH, just bad luck.
All in all, though, even in late September, we were H-O-T!! It was only 2 degrees cooler than mid-August when you look at weather.com's historical temps for Orlando. I think October and late April would be the perfect time to go to Disney, but they're also more expensive times.
Good luck!