There are several games that are not present in the US version, but their listings in the games menu can be seen with Action Replay codes. These games include:

• Bonanza Bros
• Streets of Rage 1
• Streets of Rage 2
• Streets of Rage 3
• Wonder Boy III: Monster Lair
• Wonder Boy in Monster World
• Monster World IV
• Sonic Eraser

Bonanza Bros and each Streets of Rage game are unlockable in the Japanese version but none of these games can actually be played on the US version.

In the Museum of Sonic Gems Collection, a number of classic Sonic games can be unlocked. These games start at the final boss, and can only be played for a set amount of time.

By using a cheat device to freeze the clock it's actually possible to play the entire game after the final boss is defeated.

There were originally plans to have Knuckles' Chaotix and SegaSonic the Hedgehog included in the game. The only remnants of Knuckles' Chaotix is in the game's art gallery, and SegaSonic the Hedgehog was cut due to problems with emulating the game's original trackball control scheme.