Acclaimed Flop: Though the film didn't do well in theaters at the time of release, it's still considered one of the best animated films ever made.
Executive Meddling: The Pomp and Circumstance sequence in Fantasia 2000 was inserted at the insistence of Disney CEO Michael Eisner, who had just gone to his son's graduation and wanted a song "everyone can relate to."
The pieces themselves are actually mostly excerpts, albeit re-worked to the point where the music still transitions properly. Some parts were cut for repetition (Night on Bald Mountain), or for timing/storytelling purposes(like The Firebird Suite). Still others have parts cut-and-pasted into a different order (like The Dance of the Hours). This was also the same for Rhapsody in Blue.
The most egregious example of Executive Meddling is probably the entire Rite of Spring sequence. The original Rite of Spring, is a full 35 minutes long - nearly half the length of the original film - and the excerpts used in the film play out in noticeably different order than originally intended. The entire final sequence of earthquakes, tsunamis etc., only appears once in the original piece, near the end of its first part (the full version is split into two parts). While it is still a favourite of many people, the whole editing process apparently enraged the composer, Igor Stravinsky, to the point where he nearly sued Disney.
Missing Episode: Before Fantasia 2000 was released, its promos suggested that it was replacing the original cut of Fantasia. (Assuming you don't consider it already replaced because someone did their best to edit out a blackface caricature...)
Magnum Opus Dissonance: Fantasia has been described as being ahead of it's time, because although Walt Disney planned for this to be his big film, it actually flopped and the relatively more "kiddy movie" Dumbo actually turned over a greater profit. In the present, Fantasia has been Vindicated by History, and is often one of the movies discussed as being the best of the Disney Animated Canon.
Old Shame: Sunflower, the stereotypical black centaurette that tended to the others, edited out of post-1960 prints.
Saved from Development Hell: Walt Disney's original idea was to keep on adding new segments and switching the order around, such that Fantasia would be a perpetual work in progress. The idea for a Fantasia sequel eventually took almost 60 years to come to fruition.
What Could Have Been: Walt Disney's original plan for the film, as mentioned above. Some of the segments they had considered for this were worked into the other compilation films Disney made during the '40s.
In Fantasia 2000, hostess Bette Midler mentions several abandoned concepts (it's not stated whether these are from the original or later), including a segment based on Richard Wagner's "Ride of the Valkyries", one based on Jean Sibelius's "The Swan of Tuonela," a "bug ballet", a "baby ballet", something inspired by the Polka and the Fugue from Schwanda the Bagpiper, and Destino, directed by Salvador Dali, and featured alongside Fantasia 2000 in its DVD/Blu-Ray re-release. It was referred to as a "baseball ballet", though it actually has very little to do with baseball, save for a couple of shots towards the end (it's a Salvador Dali piece - it's very random).
The flamingos from "Carnival of the Animals" were originally meant to be the ostriches from "Dance of the Hours"; however, Roy Disney felt that it would be too familiar. Also, flamingos look better playing with yo-yos, because they are pink!
Fantasia 2000 was originally going to include Dance of the Hours and Nutcracker Suite. A glimpse of Nutcracker can be seen in the original trailer.
Can you imagine if the Disney execs had followed through with their original idea for Fantasia and continued to release sequels to it periodically, even yearly, with brand-new music and animation? Unfortunately, the onset of World War 2 and the lack of enough money made at the box office from original film (it made a lot of money, but certainly not enough to justify the cost of making a continuous series) resulted in the idea being dropped in what is considered the most haunting Disney couldabeen of all.
Fantasia 2006 (which was to focus on world music) was not only planned, but segments were completed for it before the plug was pulled. They subsequently became standalone shorts: One by One and The Little Match Girl are included as bonus features on the special edition DVDs of The Lion King II and The Little Mermaid, respectively; Lorenzo screened before Raising Helen in theaters, and Destino has appeared at film festivals and, curiously, cruise ship art auctions. They all appeared at a 2008 Los Angeles screening hosted by Roy Disney as well.
The Sorcerer's Apprentice was also different - earlier in production, plans for the Sorcerer's Apprentice had either Dopey or Donald Duck as the Sorcerer's Apprentice.
The mythological piece was originally supposed to be set to the score from Gabriel Pierné's "Cydalise et le Chèvre-pied." They had a hard time fitting the animation ideas in with the music so they went with Beethoven's Sixth over conductor Leopold Stokowski's objections.
Someone with a keen eye for details or a photographic memory can spot some re-used animation in The Black Cauldron from "Night on Bald Mountain". The scene? When Henwen is scrying, you can spot some skeletons-on-horses from Fantasia.