Since many of the major ones I liked have been mentioned (monorail to every resort) I will take a different tack.
Policy changes:
1. Stop treating WDW as the black sheep of the Disney empire. I don't have anything against
Disneyland Resort but it sure is frustrating that they get all the best rides first and years before WDW. When WDW does finally get the ride, it is a down-graded copy. How about new rides be built a both parks simultaneously and identical copies?
2. Any new theme park must not have plans for a canal/waterway as it always turns into a swamp/moat within the first year. AK would have been so much better if they hadn't built that swamp.. I mean moat.. I mean canal around the Tree Of Life and instead had built an actual huge walkway to handle the hordes of people trying to get from one place to another. AK is very badly designed with long narrow walkways that thousands of people are trying to navigate. What is this, Seaworld?
Attraction change: Hall of Presidents.
I would like to change the Hall of Presidents from the lamest and most under utilized technology to something worthy of the name Hall of Presidents. The last time we went it was a 15 minute filmstrip (filmstrip? Didn't those die out in the 70's?), 5 minutes of each President saying their name, and then a 5 minute lame speech from George W. Bush. I'm sure the new version will be the same except Barack Obama will be giving the lame speech.
The United States has a rich history of Presidents so the show would revolve around a particular President talking about the experiences during their presidency. Other Presidents could also interject with their similar experiences. There is enough biography about each to find very interesting things without having to get too controversial. Also instead of the same show for 6+ years, there would be around 10 shows made focusing on different Presidents and it would change every showing. It is just a matter of running a different program of movements and playing a different recording. Check the schedule for which show number at what time. It would be similar in feel to American Adventure but it would focus on issues of the presidency.
Finally, Disney would plan ahead during presidential elections and have the new President done and ready for installation on Jan 19th overnight and reopen the attraction on Jan 20th at 1pm with the new/continuing President.