We were at WDW for our first trip last fall. Sept. 24th-Oct.1st.
Crowds - Friends of ours were there at the same time by coincidence. We went to the MK on an EMH day and they did both an EMH day and a non-EMH day. They said the difference was HUGE. They did the whole park twice in one non-EMH day. This was with their DS4 and DS2. When we went to MK on a day with amEMH the crowds started to pick up in the afternoon and we used FP for things like Splash mountain. We also had some lines in the morning in Fantasyland (Dumbo, Ariel's grotto), but walked right onto PeterPan, Small world, and Philharmagic. I know that this is trivial to people who travel at peak times, but our friends LOVED the day when it felt like they had the whole park to themselves and could ride the same ride over and over again. At Epcot, world showcase was busy, but more like a mall on a Saturday than anything. Not bad. We used FP for soarin, but walked right onto Nemo and there was only a 5 minute wait for single riders at Mission Space. We also walked right onto the Safari at AK and into everything but ToyStory Mania at HS. AK and HS were on non-EMH days, so I really think this makes a difference and will keep it in mind when we have the chance to go again. It certainly makes travelling with little ones who don't want to wait easier.
Weather - HOT HOT HOT. Now we are Canadians who moved "down south" to Boston, so that alters our perspective, But the afternoon heat was too much for us to handle, so mid-day breaks were essential. If we were doing it again at that time of year I would make our character meal ADRs for lunches to get a nice break form the heat instead of dinners. We did this at Akershus in Epcot and it was the best way for us.
I would suggest moving your stay up a week if you can though. When they announced Free Dining last year we missed the check-in by 3 days, but we already had our airfares booked and the change fees didn't make it worth the bother to also change (and possibly lose) our ADRs. When looking into it after the fact I discovered that traditionally Free dining does not always cover that last week of September. It probably has something to do with the F&W festival. Trust me, it's a real bummer to miss such a nice deal by only a couple of days!!!
Have a great trip!! Wish we were going back too!