Executive Meddling: The whole reason the game gave Knuckles the spotlight and replaced Sonic with Mighty the Armadillo was because Sega of Japan rightfully feared that the 32x (and thus the Sonic game being made for it) would be a flop, and didn't want to give Sonic top billing out of fear that it would hurt the series brand image if the game tanked.
"Wechidna", for the Dummied Out character called "**********" by the game, because he appears as a glitched, white Knuckles. Research on the game's prototypes eventually revealed he actually was Tails.
Also, "Metal Sonic Kai" or "Mega Metal Sonic" for the game's final boss. Contrary to popular belief, that was never its name - Metal Sonic Kai is actually the name of the ordinary Metal Sonic in this game according to the Japanese manual, whose body has been reconstructed since his last encounter with Sonic.
It's speculated that the two robots Heavy and Bomb's true nature was to slow the heroes down for Robotnik sabotaging their success, Possibly why there the joke characters in the game and among the fanbase. This is suggested by there downgrade abilities such as Heavy's inability to jump and Bomb explodes when he takes hit damaging the player, also seeing that the characters are never seen or mentioned in the franchise again.
There is evidence that this was originally going to be the cancelled title, Sonic Crackers. More specifically, the ring tether mechanic was present in a working form and the animations used for Mighty are very clearly drawn over Sonic's animations from the Crackers proof-of-concept (he even has the same Wheel o' Feet effect despite his primary character trait being his strength). Furthermore, the level music from Sonic Crackers had become the game's leitmotif.
If you get hit several times in a row in Crackers, your character becomes stunned for a while. Similarly to the slamming-on-walls quirk from the Sonic 2 betas, this was cut from the game.
It was originally going to be included in Sonic Gems Collection at one point, but was dropped, probably because of issues emulating the 32X. However, an entire mini-gallery of art from the game was included in the Museum.
One beta screenshot of the title screen implied that Espio was supposed to be the main character or a major player of the game, with Knuckles just tagging along. He's given top billing in an early title screen, and the opening graphics to each level still put Espio's name over Knuckles in the final game.
Other staple mechanics from the Sonic series were intended at points in development. Data and artwork for loop de loops and water areas still exist in the final game but were left unfinished (a likely explanation for the game's more limited level designs).
As mentioned above, glitches versions of what seem to be Tails exist in prototypes of the game. Mighty's blatantly tweaked sprites from Sonic's Crackers art suggest both characters were intended to be playable early on before making it at A Day in the Limelight for Knuckles.