NES had Pacmania and Gamecube had Pacman vs, Namco has also had a few first party, non-Pacman games as well, like that fucking Soul Calibur Legends game. And while there hasn't been a first party game explicitly featuring cloud, Square has had a few first party partnerships with Nintendo, ie. Super Mario RPG.
Character additions in smash are typically the result of close business relations with other developers, if it was a popularity contest then we'd be getting a lot shittier characters