At a panel, Warren Spector mentioned that he limited the references to other Disney films up to The Jungle Book in order to prevent himself from going overboard. At the same panel Peter David mentioned that The Jungle Book was, incidentally, the last film Walt Disney had a direct hand in making. Warren then replied that that was now the official reason.
Christmas Rushed: Word of God is that Epic Mickey was rushed to reach store shelves by the 2010 holiday season, which explains a few of the game's rougher edges. Even with the rush, it still missed the "Black Friday" after-Thanksgiving shopping weekend.
Collectors Edition: Those who pre-ordered the game got a special edition of the strategy guide (with an interview with Warren Spector in it), themed Wii skins, and a vinyl Mickey figurine holding a paintbrush.
Executive Meddling: Disney ordered the game to reach store shelves by the 2010 holiday despite it still having about a year of estimated development time before it was completed. Beyond that, they were actually pretty hands off with game, only stepping in when they believed things got too dark.
Showing up in Disney Theme Parks after the game's release was a lot of merch featuring old Mickey (including at least one shirt featuring a shot of him from Gallopin' Gaucho, a short that fell into company Canon Discontinuity for having Mickey light a cigarette with his foot among other things.) This game is why.
Screwed by the Network: the finished game was originally supposed to be a late 2011/December 2011 release, but Disney cut the development time by a full year for the 2010 holiday season, meaning the game technically isn't finished.
The "Scrapper" mechanic (where Mickey's appearance would change to reflect the player's moral decisions) has been... scrapped. Depending on whether Mickey's actions were good or bad, his appearance would have changed into either the tall and proud "Hero" form or the dark, hunched-over "Scrapper" form. Even before these were cut from the game, there were two other, much more evil-looking forms proposed (one of which you can see in this concept art◊), that would only be attainable if the player took the worst actions possible. Spector said that people didn't like having Mickey's iconic appearance tampered with, so instead his Fairy Companions turn blue or sickly green. The change from the Scrapper/Hero system to Guardian system was also made so people wouldn't just try to play the meter and instead make their own choices. More concept art regarding the mechanic can be seen here for those interested.
Before the concept of Mickey using the paintbrush was finalized, many sketches and ideas of Mickey's paint abilities were of him using himself as the paint, ink constantly dripping off him and even some drawings having parts of him reduced to a sketch due to how much paint he was using.
An Alice in Wonderland level based on "Alice's Curious Labyrinth" from Disneyland Paris was planned but scrapped to avoid confusion with the Tim Burton film. This is actually referenced In-Universe; it's in Yen Sid's model of the Wasteland, but when Mickey spills the thinner onto the Wasteland, the Labyrinth model sinks away into nothingness, erasing it from the game.
Oswald was originally going to be the main antagonist of the game, with the Final Boss being him fused together with the Shadow Blot to become the "Storm Blot". When Warren Specor came on as director, he made the decision to turn Oswald into an Anti-Hero since he wanted people to love Oswald again, not hate or fear him.
Several concept art shows that Minnie was originally going to be in the game.
Another storyboard shows Ursula◊ as a villain in the story. According to the Art Book, Ursula would have lived inside The Jug, originally written as a separate location from Mickeyjunk Mountain attached to various machinery filtering out the thinner in the environment.
Potential bosses for Mickeyjunk Mountain included Chernabog and a robotic Yeti exo-suit of Oswald's.
A larger example comes from the decision why the game is a Wii exclusive. It was originally a XBOX 360/PS3 game, but when he was asked about a Wii version, Warren Spector decided he didn't want to it to make it a bogged-down port. So they decided to make it a Wii exclusive.
The Phantom Blot would have appeared as a separate character from the Shadow Blot, but it was decided to only have the Shadow Blot because of concerns that players would be confused as to which Blot the characters were talking about.
Unfinished videos for "balloon" and "fireworks" sketches can be found in the game's files.