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Just a very brief reminder that Ultimate originally was going to cut a good chunk of Smash 4's full roster for the game but Sakurai decide to put the effort to bring everything back for just one game.
If Mewtwo's twice base game cut wasn't anything evident, they don't care if you were the most popular shillmon for the time, you'll still get the boot once they run out of development time.
Hope that answers your question, OP.