In mid-2007, veteran developers Gearbox Software came up with the idea to port the game to the Wii console, and upon Sega's approval, began working on the new version with Sonic Team as consultants. The default setting of the game uses the Wii Remote and Nunchuk to simulate the maraca-shaking from the original game, with the option to use two remotes for completely wireless play. Optional maraca-shaped attachments are also available to provide the full experience. Unlike the maraca controls of the Dreamcast version which could detect the height at which they were shaken, the Wii sensor bar is not capable of this. Instead, the angle at which the Wii Remote is being shaken determines if high, mid or low notes are hit. The rotation of the controller also has an effect on note detection, especially when doing cross-over moves.
All the characters and stage designs from the original game return with enhanced graphics. Many of the additions from Ver.2000 that were not available to people outside Japan are included, such as Hustle Mode and the new character Amiga. A "Career" mode exclusive to the Wii version is included, consisting of challenges in which players must clear songs to earn various unlockables, including maraca effects and additional songs. Unique to the Wii version, new stages based on other Sega games were added, including ones based on Sonic the Hedgehog and Space Channel 5, complete with cameos of Sonic and Ulala respectively. Nearly, but not all the songs from the original game are included. It also includes many of the songs from Ver.2000. 23 Wii-exclusive songs were added, bringing the total to 44. The game supports Miis and displays them next to the player's score as well as showing two random ones in-game during stages. Their expressions change based on performance (Bad, Medium, or Good). Online leaderboards and friends lists let players post their best scores and compare them, but only when an original, player-created Mii is used. This feature cannot be used with the guest Miis.
In addition, downloadable songs are available for an extra charge. These additional songs come in download packs. The first pack includes the songs "I Want Candy (cover version)" by Bow Wow Wow, "Are You Gonna Be My Girl" by Jet, and "Mambo Mambo" by Lou Bega (all master tracks), and were available upon the game's release. Download packs come in sets of 3 and cost 500 Wii points. As of December 2008, three download packs have been released.