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.
Rite of Spring, filled with Stock Dinosaurs (including the T. rex) of different Mesozoic periods and sometimes-questionable anatomy. In fact, Tyrannosaurus lived closer to when humans live today than he did to when Stegosaurus lived. According to commentary on the Blu-Ray release, the fight was originally to have between the T-Rex and a Triceratops, but the Stegosaurus was switched in as the animators felt the thagomizer would make the battle more interesting.
Awesome Music: It's a given - this was part of the point of Fantasia anyways.
Big Lipped Alligator Moment: The Carnival of the Animals, Finale is the shortest part of Fantasia 2000, and it's far more silly and slapsticky than any other portion of the film. Even James Earl Jones doesn't know what to make of it.
Bowdlerize: Whereas the original Fantasia segment has Yen Sid swatting Mickey with the broom after his little stunt, at least one of the storybook adaptations avoids this. The sorceror simply tells Mickey not to start what he can't finish.
Then there's the horde of baby bunnies scampering off the ark.
Hilarious in Hindsight: The introduction to the Rite of Spring segment has Deems say that dinosaurs had the brains of pigeons. Be more accurate to say the reverse, nowadays.
And in the introduction to the Nutcracker segment where Deem states that nobody performs the ballet nowadays. Skip to 70 years later where said ballet is arguably the most well-known and most performed ballet in the world.
Lighter and Softer: 2000, with its celebrity guests and happy humorous fare like Pomp and Circumstance and The Carnival of the Animals, Finale, is considered to be somewhat less adult than the original.
Magnum Opus: Considered one of Disney's top contenders, and was originally intended to be as such by Uncle Walt.
Sequelitis: The general consensus of 2000, though it's still quite well received on its own merits.
Spiritual Successor: Many of the shorts in 2000 are meant to mimic shorts in the original: Symphony No. 5 suggests Toccata and Fugue in D Minor, Pomp and Circumstance recalls The Sorcerer's Apprentice, The Carnival of the Animals, Finale mimics Dance of the Hours, and Firebird Suite clearly parallels A Night On Bald Mountain/Ave Maria.
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. Fortunately, as of 2014, the "Lost Notebook" has finally been released to the public by author John Canemaker.
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.
The Woobie: Pretty much everyone in the "Rhapsody in Blue" segment, Jobless Joe especially.