Alex, Nina, Harry, and Kate are no longer playable in the Virtual Console version of the game. None of the character's personalized courts (excluding Donkey Kong's) can be unlocked either. This due to the game needing to be connected to the Game Boy Color version of Mario Tennis to unlock this content, which the Wii cannot do.

If the player turns on the game without a controller plugged in, a humorous screen featuring Luigi and Waluigi will appear with the "Match Point" theme playing, along with a message prompting the player to reset the game with a controller plugged in.

If Mario is not one of the characters on the court, he will appear as the referee. However, if Mario is one of the players, the referee will be either Toad or a blue version of Mario. The latter is a reference to Tennis for the NES, where Mario also wore blue as the referee.

The ring tournament mode was removed from the Virtual Console version of the game for unknown reasons.

Waluigi was created as a rival to Luigi. There were also talks of a Princess Peach counterpart to further expand the roster. This proposed "Warupichi" character was ultimately dismissed by Miyamoto.