In addition to the console Anniversary Collection, a Game Boy Advance counterpart was also planned. Originally named Mega Man Mania, the title would have included colored remakes of the five Mega Man games created for the Game Boy, along with a History section and artwork. The compilation was planned for a Q4 2004 release, but was repeatedly delayed, partly due to Capcom reportedly having difficulty in locating the source codes for most of the games, forcing them to recreate them from scratch. In January 2006, it was announced the compilation was being "placed on indefinite hold" as Capcom and gaming retailers began issuing pre-order refunds.

Both the GameCube and PlayStation 2 versions of Mega Man Anniversary Collection were created within the same period. This would explain why some of the graphics for the PlayStation 2 controller buttons are present in the files for the GameCube version.