Like all the posters said before me, way, way hot and humid. The humidity is probably the key word here, since 90 degrees feels like 103. It's imperative that you keep yourself hydrated. Drink lots of water, even when you think you're not thirsty.
Florida does tend to get thunderstorms in the afternoons in September, generally between two p.m. and five p.m. They don't last long (maybe an hour for any one particular area), but they can be severe and not a situation I'd want to be in walking around outdoors with the lightning. We use this time to shop indoors or head back to the hotel to recharge a bit.
Plan to sweat...an awful lot. When DH and I go in September (which is our wedding anniversary month, so we always hit Orlando, even if it's just for an overnight trip), I bring waterproof mascara and lipstick, that's it. Everything else just melts within a few minutes. This is true even at night.
I don't even worry about my hair. I tie it up and plan on having to re-tie it several times over the day from all the sweat. I also cover it up with a big visor or hat, depending on whether it's daytime or nighttime.
The ground is about as hot as it's going to get in September. I find no matter what shoes I wear, my feet are sorer than any other month we go in. Personally, soaking them in hot water -- perferably a jacuzzi somewhere -- fixes them in about five minutes. If there's no jacuzzi, DH and I soak them in the tub in our room after showers while we sit on the tub ledge (nice visual, eh?).
Hurricanes, ugh. After the past couple years, I think Floridians now realize it's our turn and the Carolinas get a break! Once you're there and a hurricane is threatening the Orlando area, I think you'll be safe. For us, it's the trip to and from that we become concerned about, since we're already in Florida and we drive. Just watch the weather and forecasts and try and be flexible in case you need to stay an extra day at WDW or come a day late.
The weather is just going nuts everywhere, no matter what part of the world you live in. At least with a 'cane, you can see it churning out there on the news days in advance. As it gets closer, the weather folks are pretty good about predicting what it will do. I don't know how other Floridians feel on this board, but during hurricane season, watching our local weatherman every night is a "must do!"
When it gets a little closer to your trip, bookmark an Orlando local news station to see what's being advised. We use the WESH website, which has a live feed/telecast.
