In a screenshot of the Story Selection screen, we could see that it was planned that there were to be stories for Big, Omega, and Espio. They're plots were unknown, but Big's was obviously going to have something to do with Froggy going missing. It is unknown why these stories were scrapped out.
It was also announced that there was going to be a level before the boss in the Final Arena zone. But it was removed for unknown reasons.
There were going to be guest appearances by Aiai, Amigo, NiGHTS, and Billy Hatcher as playable characters in multiplayer mode. But the creator wanted it to be only in the Sonic series, so they were removed.