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 Wii Virtual Console version of the game due to the online leaderboard being shut down. Its icon is still there, but it is skipped over in the menu. It was implemented again in the Wii U Virtual Console release.

Waluigi was created by Camelot artist Fumihide Aoki during the development of Mario Tennis 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 Shigeru Miyamoto and Nintendo because they were hesitant about making an evil version of Princess Peach, given how she was still portrayed as innocent in earlier games. Despite this, Aoki would keep the character idea around for Mario Power Tennis, featuring another rejected design that would eventually be revealed to the public in 2023, both through unused sketches and a 3D model. In one sketch, the character wields an axe, which according to Aoki, was added to make her "cute and scary". Aoki also revealed more information through Instagram comments, like how "Warupichi" was going to be the authority figure that gave orders to Wario and Waluigi, and how he wanted to make a companion to "Warupichi" that would have been an arch-rival to Yoshi that was going to be a dragon with horns and wings. The day after revealing Warupichi and the rest of this information, Aoki deleted the original posts and locked his Instagram account.

The September 2000 issue of Nintendo Power contains a "Nintendo Power Online" section on page 12, featuring an article titled "Mamma Mia! It's Waluigi!" The accompanying text introduces Waluigi to readers, reveals that he has his own website: www.waluigi.com, and claims to have an upcoming online game called "Waluigi's Toenail Clipping Party".

At the time of the Nintendo Power issue's release, www.waluigi.com was identical to the official website for Mario Tennis, www.mariotennis.com. One of the files hosted on the Mario Tennis website was the Adobe Flash file "toenails_coming.swf", which is an advertisement for the game instead titled "Waluigi's Foot Fault" depicting him showing his bare feet and unkempt toenails (he also occasionally blinks). Another file hosted on the website was "toenails.swf", which was supposedly the game itself. Catalogued alongside this file are two additional .swf files named "paint_the_lines" and "deface_painting", which could be evidence of other Flash games hosted on the Mario Tennis website.

However, the waluigi.com domain has since been turned into a redirect to the official Nintendo website. The toenails.swf file was not preserved, and as of 2023 has not resurfaced.