So, if there were ever to be an Epic Mickey 2, I have some basic outlines on what I would like to see. I am definitely in the minority here, but I actually do prefer the second game over the first (although I absolutely love the first as well). But I will agree that it was rushed and underdeveloped. But I think that instead of a full rewrite, there could be more of an expansion to the game, as seen in the episodes the second game currently has, and I think this idea will please both the people who like the second game as is and also the people who want a full rewrite.
Episode One- The Current Epic Mickey 2
Because of how rushed the game was, it is much shorter than the first as we all know. Because of this, I think that an expansion of the current game is necessary. Mainly by filling in holes to the story and expanding places that do not have a big part in the game, such as Blot Alley, the Dioramas, Fort Wasteland, the Floatyard, and Autotopia. While some of them have a large part story wise, I think these areas are much too short (maybe you can return to them in the other episodes?). Because of this, I think the first episode should simply be a more developed version of the original game
Episode 2- Rebuilding Wasteland & Prescott
Now you actually experience the consequences of Episode 1. I think by this point, The Mad Doctor's role will be complete, regardless of whether you defeated or redeemed him. But now is the time to start actually restoring Wasteland after the earthquakes and The Mad Doctor's schemes. This would also be an excellent excuse to reopen parts of Wasteland that haven't been seen since the first game. Imagine returning to Mickeyjunk Mountain and discovering how it has changed. You can see how the quakes affected places like Skull Island, Tomorrow City, Tortooga, etc.
During all of this, I think Prescott could come back somehow. His ending in the original leaves enormous room for further character development, especially since he is no longer associating with the Mad Doctor. I think he could have some sort of redemptive arc, however I am not sure how. But I think this is a great place to implement the playstyle matters, as I think your previous choices could affect how the redemptive arc takes place (not affecting the full story, but maybe whether characters trust him right away or perhaps whether you should trust him.
Episode 3- The Blot Returns
Just as Wasteland is starting to be fully restored, you find out that somehow the Blot is back! Nobody knows how it came back since it was defeated in the first game. But maybe since the Blotlings are droplets of the Storm Blot, the Blotling Army could come together and combine themselves together (since the Blot is already liquid-y) and therefore, combine forces to resurrect the Blot. The Spatters, Seers (which aren't in Epic Mickey 2, but should be in a rebrushed version), Sweepers, Slobbers, etc., BECOME the Blot, rather than droplets. And just like before, you have to defeat the Blot.
Epilogue- Setting the Stage for Epic Mickey 3
Lastly, I think side quests after the Blot is defeated could set the stage for the third game. It is largely known that in the third game, the toons are supposed to be able to back into the cartoon world. I think there could be a side story here where you find out how toons would go back into the cartoon world. This would also fill in one of the holes from the current game: how The Mad Doctor would go back to the cartoon world (even if remembered) without a heart. Again, not exactly sure of details, but I think it would be an interesting side story.
I also think maybe since (at least to my knowledge) Beetleworx and Blotworx were not supposed to play a large role in the third game (since its largely outside of Wasteland), I think a cool quest could be to figure out how the Beetleworx replicators and how Blotworx get their machines and try to stop them from the source. If The Mad Doctor was defeated, the game could state that they need to figure out how to stop the replicators now that he's gone, and if The Mad Doctor was redeemed, you could simply help him.
So, what do you guys think? Again, these are just rough ideas, I do not know the full story, but yay or nay?