Samantha,
A longtime October traveler was I until I experienced September. I miss the Food and Wine Festival that way, but if crowds are your concern, you couldn't make a better pick.
We found the following when comparing October and September: There IS more rain, no way around that. But it didn't get in the way of our fun. A lot of those "it's time" showers, where it's sunny one minute, pouring the next, sunny again in a half hour.
The park hours tend to be shorter, although not much shorter than October. We found we didn't care, because we could get so much done with the low crowds, we didn't care about a lost hour or two.
In preparation for our June trip, we've been watching a lot of last September's home video. I was making so many comments about how empty MK was on Wednesday. In Epcot, we rode Test Track with a ten minute wait, and in MK it was fifteen one time for BTM. Those were our two longest waits.
Walkons included Splash Mountain (two straight times on Wednesday), everything in Epcot on Sunday, Space Mountain on Wednesday (in retrospect, Wednesday was a great day to be in MK), Buzz Lightyear (yeah, Wednesday), everything in MGM on Tuesday, with the exception of TOT and RRC, which were both five minute waits.
The neatest surprise was Typhoon Lagoon. We'd never been because we weren't into it in October, and in June, another travel time of ours, we saw the crowds and bagged it. What a delight this place is on a weekday in September! We were able to go many places in Epcot without a PS. There were specials in the Disney Stores, cheap hotels, seats on all the busses, and plenty of characters for all.
Am I jazzing you up for September? I hope so. What a wonderful time. We HATE crowds, we HATE high prices, and we go in off season to avoid all that. But my wife has always felt jipped in October when the daytime temperatures don't get out of the sixties (which can happen) and the nightime temps hit the low fifties (which often happens). Many people like October because it's a little cooler. Not us. We love the heat. Our vacation dollar went further, and we were more relaxed because we did less waiting in line, leaving more time for alternative activities and leaving us completely oblivious to the lower park hours.
WARNING: All of the above doesn't apply to MK on Saturdays. Usually the only day for Spectromagic and FITS, it looked like the 4th of July around 7 PM. If you want to see the fireworks, go in around 6 and deal with it for a couple hours, or else watch from the Poly Beach. And do take the opportunity to tour MK after closing. With the low attendence, Wednesday night after close was something special.
If you do it, do it with confidence. And enjoy! If you have any detailed questions, September in Disney is my favorite subject.
Pat