These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
One YouTube comment brought this up regarding Zeus/Jupiter's behavior in the Pastoral symphony. He seemed to be going specifically for Dionysus/Bacchus with his lightning bolts, never seeming to actually hurt anyone else. The commenter said that maybe Zeus was just being a Jerkass god like he's normally been portrayed, disrupting a festival for no reason other than it amused him... or maybe he was simply trying to test his son in his own... unusual way by interrupting a celebration when he'd least expect it.
It also helps that, since Dionysus/Bacchus is just as immortal as his father, it's not like the lightning bolts will actually hurt him (the unicorn donkey is another story). He's not putting his son in any actual danger.
Awesome Music: It's a given - this was part of the point of Fantasia anyways.
Values Dissonance: Sunflower, the servant centaurette in "The Pastoral Symphony", whose human half looks like a black "pickaninny" and who performs menial tasks for the white-featured centaurettes. Deleted from all releases since 1969, so most modern viewers haven't seen her. If you're curious, there's YouTube.
even worse, she's actually animated in the style of the "Black Face" minstrel shows that were halted by the civil rights movement, which took place at around the time the censoring was implemented.
On a less offensive level, the dancing mushrooms, which are clearly made to resemble old-fashioned Asian caricatures with slit-eyes and those funny cymbal-shaped hats. Granted, given that the title of the sequence was "Chinese dance..."
Chernabog's demons avert Barbie Doll Anatomy. The centaurs play it straight, but are still topless women.
Visual Effects of Awesome: One of the late Walt Disney's greatest pieces of animation. Some of the special effects were so spectacular for the time that film historians were at a loss as to how they were created. Disney themselves had few clues, as the camera team dismantled every rig immediately after shooting and kept no official record of what they had done. Fortunately, one particular technician, named Herman Schultheis, kept a private record of every effect he worked on and this notebook was rediscovered in the 1990s, revealing the complex - and quite inspired - filming techniques the team employed.
What Do You Mean, It Wasn't Made on Drugs?: The film counts, it starts off with surreal geometric shapes, followed by a seasonal fairy pageant with flowers, mushrooms and fishes, followed by MickeyMouse animating a broom, followed by the evolution of the earth into the end of the Mesozoic era, followed by Classical Mythology, followed by an animal ballet and ending with THE DEVIL and his demonic hordes and a church chorus walking through a forest to a rising sun.