The game pays homage to other JoJo-related media that came before it; in this case, the OVA:

• One of Avdol's alternate color schemes turns his coat red and shirt to yellow, similar his appearance from the 1993's and 2001's OVA. The same goes for Joseph Joestar, Polnareff, and Black Polnareff, all of them having alternate color schemes that resemble their OVA apparance.
• One of Iggy's special moves make him create a giant wave of sand in his opponent's direction, similar to how he attacked Vanilla Ice in the OVA.
Contributed by ZpaceJ0ck0
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According to early concept art, more characters from part 2 of the JoJo manga series were planned to be playable, including Stroheim, Kars, Esidisi, Wamuu, and Wired Beck.
Contributed by MrConnman123
Besides being based on Part 3 (Stardust Crusaders), this is the first game to have elements from more than one JoJo saga:

• Part 1: Wang Chan as Shadow Dio's "child" form during Alessi's stand ability, a shot of the Stone Mask appears when a character is stand crashed, and both versions of Dio have Space Ripper Stingy Eyes as a special move.
• Part 2: Young Joseph is a playable character, Caesar appears in the Young Joseph's special move that contains several manga panel flashbacks as well as Lisa Lisa doing the same for Old Joseph's version, the Red Stone of Aja is used as one of Young Joseph's supers and the crossbow he used against Wamuu, as well as the coke bottle during his introduction scene, appears in his moveset.
• Part 4: The arrow appears during Polnareff "Requiem" super, one of Jotaro's alternate color scheme recolours his coat, hat and pants white, much like his Part 4 outfit and in one of Dio's alternate color scheme, The World is pink and blue giving it an appearance similar to Crazy Diamond.
• Part 5: Silver Chariot Requiem appears as a super combo for Polnareff and one of his win quotes translates to "We'll meet again in the future...in Italy".
Contributed by ZpaceJ0ck0
Performing a time stop with the characters Dio or Jotaro after an opponent has been defeated sometimes causes a glitch where the opponent remains frozen for several seconds into the next round. This virtually guarantees another loss for them, as even a single hit while frozen like this causes a large amount of damage.
Contributed by ZpaceJ0ck0
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Iggy's second special seems to be a reference to Akuma's famous Shungokusatsu from the Street Fighter franchise, also developed by Capcom. Aside from the similar animation, the game's data contains an unused sprite of the kanji for dog (犬,inu), parodying the kanji for heaven (天,ten) that appears during Akuma's Shungokusatsu.
Contributed by ZpaceJ0ck0
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NSFW - This trivia is considered "Not Safe for Work" - Click to Reveal
After beating arcade mode, a short cutscene plays of the selected character finishing DIO. In the US version DIO flies offscreen, while in the uncensored version of the game DIO instead splits apart and violently explodes, much like his death in the manga.
Contributed by ZpaceJ0ck0
The N'doul bonus stage has a dead Speedwagon Foundation helicopter pilot in the background. The character was removed from the US version of the game because not long after the start the stage, one of N'Doul's Geb water hands attacks the pilot's beeping wristwatch and cuts his hand off.
Contributed by ZpaceJ0ck0
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Creator Hirohiko Araki is known for having a strong preference for western music, because of this most characters reference a popular band or song in some way. This meant it was necessary to rename some characters to be acceptable for release outside Japan. Examples of name changes include Devo to D'bo and Vanilla ice to Iced, although some references are still included, such as Iced quoting Ice Ice Baby with "You had a problem.... I just solved it." in JoJo's Bizarre Adventure: Heritage for the Future.
Contributed by ZpaceJ0ck0
N'Doul (or N'Dool in the localized version of the game) was originally planned as a playable character, artwork exist that show how he would have fought, along with an Alessi form. It's possible to hack the game to choose N'Doul as a character, showing that a number of assets still exist in the games files, such as an alternate colour, animated life bar portraits, animated super move and VS screen portraits and a cut-in for the "Here Comes A New Challenger!" screen.
Contributed by ZpaceJ0ck0
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The games data contains sprites for Joseph using his Hermit Purple as a grappling hook, which was likely intended for a mid-story cutscene, Spoiler:when DIO is chasing Joseph around Cairo, which would closer match the anime and manga.
Contributed by ZpaceJ0ck0
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In the international version, Chaka's blade is coloured brown while in the Japanese release, it is silver. However, Khan and Black Polnareff's swords remain unchanged in both versions,Spoiler:despite the fact that all the 3 characters are technically using the same sword in the storyline.
Contributed by ZpaceJ0ck0
Sho Hayami, the voice actor for Vanilla Ice in the original game, later reprised his role in the animated adaptation of JoJo's Bizarre Adventure: Stardust Crusaders, over 15 years later.
Contributed by Frank Jaeger
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In the 1993 JoJo RPG for the SNES, Midler was portrayed as a stewardess, making it the first time she had a physical appearance. Seven years later, when Capcom was producing JoJo's Bizarre Adventure, they wanted to include Midler as a playable fighter in the game. However, as she was only shown from the waist-down in the manga, and the game was a more faithful adaptation of the source material, they asked Hirohiko Araki to redesign her into something like a belly-dancer with her face covered up. Since then, as shown in the JOJO A-GO!GO! artbook, this new look is now her default appearance.
Contributed by ProtoSnake
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Unused sprites for Tower of Gray/Gray Fly can be accessed via the game's debug menu. Information for assembling the sprite is unfinished, and thus uses Jotaro's sprite assembly method instead. The sprites for Gray Fly are mostly finished, which includes various attacks and death animations.

These sprites would later be used in the PSX port, where Gray Fly is an enemy in Super Story Mode.
Contributed by G-Haven