In "Smash Kingdom", from 2007, Mega Man makes an appearance as a potential newcomer to the Smash Roster. Come 2013, "Smash Kingdom" technically predicted his inclusion in Smash Bros. as he was officially announced as a playable fighter in 2014's Super Smash Bros. for Nintendo 3DS and Wii U.
During the "Ganondorf's Kingdom" episode, Ganondorf threatens to fire Vaati and replace him with Zant. Zant and Ganondorf are in Hyrule Warriors, but Vaati doesn't show up at all.
When Super Smash Bros. Ultimate was revealed, people were speculating that Steve from Minecraft would be playable. Steve would eventually become a playable character, but technically speaking, they got "Steve" when a Piranha Plant got included, and his cousin Petey was a part of his final smash.
Geno: (Upon hearing that he won't be appearing in the series because nobody would get the Super Mario RPG references) I guess I'll have to show them why I'm so... AWEEEESOOOOOOOOME!*uses the Geno Beam*
This becomes a Brick Joke in the Halloween Episode, where one of the Alternate Endings has him come back from almost certain death to completely solo the Zombie Apocalypse.
Geno: Miss me motherfuckers? Now you KNOW why I'm awesome! *assumes Badass Armfold*