I was waiting for someone to bring this up.
Non-circumstantial examples (i.e. planned ahead of time):
Smash 64: Mario and Luigi, Pikachu and Jigglypuff
(Bowser, Mewtwo, and Dedede would have also added to this tally)
Melee: Bowser and Peach
And if you want to get technical, Zelda and Sheik, though they have the excuse of being the same individual and introduced together through a transforming gimmick.
Brawl: Meta Knight and King Dedede, Pokémon Trainer and Lucario
(Toon Zelda/Sheik was also planned as filler, so it could have been Toon Link and Toon Zelda/Sheik)
Smash 4: Rosalina and Bowser Jr.
Circumstantial examples (i.e. not planned ahead of time):
Melee: Mewtwo and Pichu (last minute clone), Marth and Roy (last minute clone), Bowser/Peach and Dr. Mario (last minute clone), Zelda/Sheik and Young Link/Ganondorf (last minute clones)
Brawl: None, but it could have been Diddy and Dixie (separate).
Smash 4: Robin and Lucina (last minute clone), Palutena and Dark Pit (last minute clone)
Notice how Sakurai has mainly avoided double-dipping in initial plans, and has become less inclined to do so over the years, with just this latest game only featuring a single double-dip that wasn't a result of certain character alts getting their own placements on the roster later in development.
Now, DLC has come into the picture for the first time in the series. This can easily change things, such as for example, Elma or Paper Mario being alongside Shulk and Rosalina/Jr. But at the same time, with how limited DLC is going to be, I don't think series are going to double-dip the DLC. I'm not expecting another Pokémon, be it another returning veteran (Pichu, Squirtle, Ivysaur) or a newcomer (Sceptile) because of Mewtwo. I'm not expecting someone like Corrin because of Roy (though to be fair, I wouldn't have expected Corrin even if Roy wasn't DLC). So likewise, I will not expect both Dixie and K. Rool.
Do I want it to happen? **** yes. But I'm not betting on it happening. That way if it does happen, it will be a pleasant surprise, and if it doesn't, I wouldn't have gotten my hopes up for nothing.