First of all, when everyone posts take into consideration that every attraction may well be someone's favorite.
Two attractions that have been mentioned in this thread already (Living With the Land and El Rio Del Tiempo) are two of mine.
However, that said there are attractions I've like to see updated or replaced:
1) The biggest blights in Epcot would have to be the Wonders of Life pavillion which is standing empty. It's a shame that they can not find another corporate sponsor to upgrade this building, 'cause one of the best ever attractions is in this spot: Cranium Command (true, some of the actors/characters in this show are probably no longer known to today's children, but that is unneccesary to the enjoyment of this attraction in my opinion).
A new version of Body Wars (perhaps using Soarin' style film tech or a simpler dark ride track with animatronics instead) would be a great addition to the mission of this park to educate.
The other blighted pavillion would have to be the Imagination pavillion. The 3D movie is no longer relevant to today's kids. The original film this is based on came out nearly 20 years ago. Most of today's kids may never have heard of it. I've heard rumours that a new 3D movie starring the Dreamfinder character from the original Imagination ride is being prepared for next year's 25th celebration of Epcot. That would be a welcome change (don't forget this would be the third film to play there with Captain EO being the first). I would also like to see another rehab of the ride (remove Eric Idle, return the Dreamfinder character...even if they can't rebuild the original ride, new segments would be just as fun I'm sure).
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In Future World, all three movies could stand to be replaced. I've heard rumour that the there is a new Canada movie being prepared and that would be an extremely welcome addition.
While I do very much enjoy the El Rio Del Tiempo ride, I've heard there is a possibility of a "Three Caballeros" rehab for this ride and I'm sure I would enjoy it, but would miss the simple charm of the original.
I would love to see the originally planned Japan Bullet Train ride added to that pavillion or some of the other rides attractions that never made it off of the drawing board (the El Rio Del Tiempo like gondola ride in Italy for example).
One thing that would be a strong improvement would be more effort in each of the countries to update some of the exhibits. I was pleased to see that there would be a new exhibit in China, but, for example, the same tin toy exhibit in Japan has been there for over two years.
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In MGM, I think the Sounds Dangerous show is a great idea, but perhaps could use a new story/film to go with it.
The Great Movie Ride generally is in the most need for rehab throughout the whole park in my opinion. The figures are either not moving, barely moving or moving strangely. I would also dispense with the gangster/cowboy thing...it slows down the ride and can be so forced depending on the tour guide you have.
The only thing I'd change about Muppets is fixing the television monitors in the pre-show area. Many of them are showing wear with blank screens and colors that are bleached.
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In AK the one thing I most would want to change is the Kilimanjaro Safari ride...I would remove the Big Red/Poachers storyline. Like the Gangster/Cowboy story in GMR it can be forced and many times cuts into our tour guides showing us the animals because they get interrupted by the pre-recorded radio messages.
While some don't enjoy the cheap carny rides at Dinoland, I appreciate how much time and effort it took to make that area look that cheap on purpose. I do like that area for distracting/keeping busy the family members that may be too intimidated by either the Everest or Dinosaur rides and need something to do. The one thing I would change is I might want to add some more carny games, perhaps another smaller kiddie ride or two and a carnival food counter service (funnel cake, fried oreos, corn on the cob, fresh squeezed lemonade, etc.).
Of course, my big dream for this park would be the addition of more continents: Australia and South America would be welcome additions with more animals to see. In Australia I'd add another Safari ride, this one themed to the outback, plus another walking trail featuring kangaroos and koalas, etc. In South America, we might see a Emperor's New Groove ride or show and perhaps another "mountain" ride through a simulated Machu Piccu. This would also be a great location for a Latin-fusion sit-down restaurant with Argentinian, Chilean, and Peruvian dishes amongst others.
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In MK, I'd most want to do something at the Stitch Encounter...it's probably time to completely flatten the interior of that ride and start a brand new attraction. To avoid over Pixaring the parks, perhaps it would be time to look at another futuristic Disney property and one that should have gotten more attention than it did considering the subject matter (pirates): Treasure Planet! I would think that there should be at least enough room in that building for a Star Tours/Body Wars style ride based around this movie. We could also see characters from this movie making appearances in the park.
Back in Toontown, I think it may be time to change from Mickey's Toontown Fair to Mickey's Toontown COUNTRY Fair and add a Legend of the Lion King/Voyage of the Little Mermaid style show based on Home on the Range. There's some great music in this film and it could be fun for the whole family and add more characters to be visited with afterwards.
I'd love to see the Diamond Horseshoe Saloon re-opened for business with shows again (whether with Woody or with other Western themed characters)...it was great to be able to grab a sandwich and a pickle and watch a show from the balcony!
The Tiki Room should be returned to it's original show...nuff said!
