I would go with September. Both time frames will not have the Electrical Parade running at all and Fantasmic and Remember will be running on the weekends only. So entertainment wise, its equal. Where September really is great is crowds. I have been that time frame twice (dd's birthday is September 10) and it was just incredible. You didn't need fastpass except on the weekends. It can be hot, but the evenings are so pleasant. As another poster mentioned, the hours are shorter (during the week) but with the lack of crowds you don't need the longer hours as much anyway.
When we have been that time frame, Haunted Mansion, Its a Small World and Mattherhorn have all been closed. HM and IASW go down to install their holdiay overlays. One year it was just HM, the other year I think it was both. And Matterhorn frequently goes down just after Labor Day. Not saying that will happen, but thought I would mention it.
You can get great deals on the onsite hotels this time of year with the "stay four nights get one night free" deal. And that might very well be offered for both of your time frames.
Good luck with your planning!