Hello Daniel! I'm not sure how much park hopping your wife would want to do, so if I were you I'd ask her what she is comfortable with and use that as a starting point. If she is up for the running around you could probably do two parks in one day. A lot is going on right now at Disney's Hollywood Studios to make way for the newly announced
Toy Story Land and a Star Wars-themed land. There have been a handful of closures of the shows and exhibits that your wife would have maybe liked to enjoy, and for this reason I would recommend choosing between the other parks. Also, it is much easier to travel between Epcot and Magic Kingdom than it is to travel to Disney's Animal Kingdom because you have the monorail as well as the bus as a transportation option. So if I were you I'd stick with Epcot and the Magic Kingdom. Here are some things going on at Epcot and the Magic Kingdom in September:
*The Epcot International Food and Wine Festival presented by Chase starts September 25th. If you have an adventurous palate, you will both enjoy sampling the delicious cuisine from the various booths 'all around the world'. There are also culinary demonstrations, cheese seminars and lots of really great food-centric activities to do.
*Mickey's Not So Scary Halloween Party runs on select nights starting September 15th. I am really excited to come out to socialize at this year's party because of the brand new Hocus Pocus Villain Spelltacular stage show. You'll also get to see my Moms Panel friend Jason K.'s favorite parade, the "Mickey's-Boo-To-You" Halloween Parade. There are many frightfully awesome characters that materialize throughout the night, and lots of candy!
Please let us know if you need any more help with planning. Make sure to stay hydrated! Have a magical Walt Disney World vacation!