A lot of locations in the game are based on San Francisco, where Sega of America's headquarters are located. Mission Street and City Escape are based on the streets of San Francisco, Route 101 and Route 280 are the names of real interstate highways that both run through San Francisco, Radical Highway is based on the Golden Gate Bridge, and Prison Island is essentially Alcatraz.
There was once a widespread rumor that Chao apparently couldn't reincarnate more than two times. It's possible for them to reincarnate potentially 255 times due to data limitations.
While it didn't directly spawn the once-common rumor of a "Sonic and Knuckles RPG", there was some speculation that said (ultimately theoretical) project had been retooled into this game.
Writer Revolt: The director of Sonic Adventure 2 was so angry at the negative reception for Big the Cat in the previous game that he took personal offense to it and put Big the Cat as a hidden secret in every stage as a spiteful act of vengeance towards everyone. Ironically, fans are amused by his cameos (even those that hated Big) so much that they brought most of the cameos back in the PC version.
Sonic was originally going to wear his sneakers from the Genesis games, instead of his SOAP shoes which enabled him to grind. The demo released along with Phantasy Star Online still has these shoes (likely before the endorsement deal had been fully inked).
Some leftover data from the Dreamcast version shows that originally the there was a Chao Playground and Chao Library planned. The Library would allow you to create new files for the Chao Adventure VMU game, but the Playground's function is unknown. Geometry data for them still exists in the PC version.
In Battle, after getting an A-Rank on Green Hill Zone, Super Shadow and Super Sonic would have been unlocked in two-player mode. All that exists are the unlock message and character select descriptions.
The game's programmed to spawn a Goal Point in stages meant to be completed by Knuckles or Rouge should you hack the game so that you could play as the other characters within those stages, suggesting that there was going to be a sort of "free play" mode where you can play as any character in any stage.