Sonic R had gone through several changes over its development process. There are several rejected ideas, level designs, and other things that were changed before the games final release. The following details several of these things.
This early box art was found on Compuserve internet servers back in 1998. The artwork here is found in the ending scene in the game. It may have been rejected as it gave away that Metal Sonic was a secret character in the game.
A YouTube channel by the name of GameHut, which was created by Jon Burton of Traveller's Tales, had shown off the earliest version of Sonic R, dubbed Version 0.1. This tech demo has a first person perspective and shows off an unused level.
Jon Burton also showed off a later version of the game which he called Version 0.3. This version has you play as Sonic without any running animations go around an early version of Resort Island.
As the first stage in the game, Resort Island saw the most coverage in the gaming press. Most notably for a large chunk of development time the stage took place at a different time of day - sunset, as opposed to what appears to be the middle of the day. In the PC version of the game the weather varies, sunset being an option for the stage, however in the Sega Saturn version all stages remain at a fixed time of day.