Ever wonder why this game has no story/Adventure mode this time around, why Mewtwo and Roy STILL haven't returned, why the newcomers from Brawl have been cut from this game, why the Ice Climbers have been cut, after having a perfect attendance as default characters since Melee, and yet the biggest clone in the history of SSB: Dr. Mario, manages to make it in this game?
Well while we have been given a semi-petty explanation of why the Ice Climbers have been, we still don't know Nintendo's "justified" reasons for cutting the rest of the characters.
So we bring you to this satisfying in-universe interpretation of why things things are so drastically different this time around in, "Super Smash Bros. 4: The Real Story".
Apparently, the reason as to why Dr. Mario is a stand-alone playable character in this game (and not a costume palette swap for the REAL Mario), is because he's actually a synthetic mole, an agent working for Master Hand. Because Dr. Mario himself has no character of his own or an original moveset, he is considered one of the biggest slot fillers ever, making him an easy puppet for Master Hand to control from behind the scenes.
For some time after Brawl's release, Master Hand plotted to keep the next game from reaching its full potential and satisfying true players everywhere (out of spite from being defeated one time too many). By doing so, he kept close tabs on more unique and original characters (who had the unfortunate luck of being clones, and were unable to compete in Brawl) who were also left out, and would do all he can to keep them from appearing in future games. These characters were Mewtwo, Roy, and Pichu.
During the pre-release era of SSB4, Master Hand had learned of the game's limited amount of space and recent character Charizard's decision to fly solo and leave Ivysaur and Squirtle behind, so he decided to claim them for his own ends. He then decided to go after Brawl's more recent clones, such as Lucas and Wolf, after learning that older characters would be able to create more original movesets.
While Mewtwo, Roy, Pichu, Ivysaur, Squirtle, Lucas, and Wolf were imprisoned by Master Hand, he decided to send Dr. Mario to fight in the newest SSB game, he would have a better advantage in winning and ever more control. However, before the game could be released, Dr. Mario's presence was discovered by the Ice Climbers. Because they already knew too much, the Ice Climbers were also imprisoned with the rest of the cut characters, while Dr. Mario took their roster slot and replaced any trace of the character data with his own.
However, while all the current veterans and untouched newcomers fight in the newest SSB game, the imprisoned cut characters fight in the shadows against Master Hand's forces for their right to fight in Super Smash Bros. for the Wii U/3DS!