Fantasia is about a devastating war and the characters involved in it, while University is much Lighter and Softer and more sitcom-ish, rather jarringly so. This becomes genius when you realize that University draws more from modern Disney output such as Disney Channel, which generally leans more towards domestic situations and comedy, while the older Disney Animated Canon that Fantasia draws from is about struggles between the forces of good and evil. The stories' tones match their primary source materials.
In 1971's Disney on Parade, Yen Sid was identified as "Merlin the Magnificent"—presumably the makers of the special weren't aware that the character already had a name due to his obscurity. This might be why they're one and the same person in the fic.
Nightmare Retardant: In the beginning of University, there is a serious prologue with Alex Russo about to risk her life, and putting a sleeping spell on her boyfriend so he is not in danger as well. As she steps out into the ominous rain, she hears a hidden being emit an Evil Laugh... that sounds like "BOOOOYAHAHAHAHAHAHA!!!"
Take That, Scrappy!: The Imagination Movers only appear in one chapter of University, and all they do is briefly get in the way of the protagonists. The author himself said that he only included them for completionism, and that they definitely won't be appearing again.
The Woobie: Many of the characters qualify to some extent, but the biggest one has gotta be Shego. At five years old, she is forced to fight in a horrible, bloody war against her will, only to see her sister get killed by the Headless Horseman, which leads to her having to burn the Headless Horseman while it's wearing her sister's head and getting Heroic BSoD from it, and all while having to take orders from the completely unsympathetic Major Monogram. Seriously, after reading all that, you will want to hug her.
