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.
Prototype Box Art
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.
Early Game Design
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.
The very first screenshots of Sonic R have an extremely basic HUD, consisting only of numbers.
A later prototype gives the game a more respectable, albeit not final, HUD. The character icons are different and the stage still takes place at sunset.
The background consists of mountains in these prototypes, while in the final there were replaced by smaller mounds.
...except in this screenshot, where there doesn't appear to be a background at all.
A later prototype in two-player mode. The time is right but the icons are wrong, and the draw distance (and geometry fogging) seems to be worse.
The blank gold wall in the background should have a slot machine.
The trail after hitting a speed boost is yellow instead of a large array of colors.
The icons for the unlockable metal characters are different. It's possible the magazine made this change.