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The first thing I thought when I saw Zoroark in 2010 was that they made him specifically to be in the next Smash to replace Lucario and rep Gen V. That way they could bring Mewtwo back for a total of five slots (Pikachu, Jigglypuff, PT, Mewtwo, Zoroark).
Gen IV came earlier than everyone expected, though, so Zoro has to be replaced by a Gen IV mon so that they can represent X&Y. But they devised a brilliant plan to make Mewtwo come back AND represent Gen IV through his Awakening Forme. Now the roster can maintain the balance planned and Gen IV can be represented through Mewtwo's final Smash or however they implement it.
TL;DR Newtwo was invented so they could keep Zoroark in the next Smash.
Also if you disagree that Zoroark is the best choice for Gen V, my argument is still valid if you opt him for Genesect or Victini. But you know Sakurai would just be all over using some sort of gimmicky playstyle with Zoroark's Illusion.
