Nickelodeon All-Star Brawl notably has certain side characters (Helga, Nigel, Hugh, Reptar, Oblina) featured without their series' respective protagonists (Arnold, Eliza, Jimmy, Tommy Pickles, Ickis) - what is less known is that these protagonists are completely absent from the game in any physical form, with none of them appearing in stage cameos. Tommy and Arnold do make brief cameos as photographs in props on the Teeter-Totter Gulch stage and one of Helga's attack props respectively however.

Also of note are Raphael and Donatello, a half of the Ninja Turtles who are not playable in the game despite their equal importance to Leonardo and Michelangelo, with Shredder and April in their place. They do feature as a profile icon, but are absent from the Teenage Mutant Ninja Turtles stages.