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Let me explain: The second to last row is reserved for characters that were not planned for the initial finalized roster, or were of incredibly low priority. For sure, Dr. Mario, Dixie Kong, Impa, Dark Pit, and Lucina are clones or semi clones. However, there is quite a story with Ridley and Mewtwo.
I cannot say with much certainty if they were the last characters added to the roster, but my guess would be that they were put down there in order to avoid ruining the structured order of the CSS. Mewtwo could have been added after receiving a ton of requests to bring him back, and thus was placed here in this row to avoid moving around the roster too much.
As for Ridley, my guess is, Sakurai had an idea on a unique gameplay mechanic, but due to the length of time to create a 100% unique moveset to satisfy the unique functions, decided to take two shortcuts. First, he had Ridley borrow a number of moves from Charizard; the second was the removal of aerials altogether, and I'll tell you why: Because Ridley is strictly an aerial fighter, he is never actually on the ground and is thus always hovering. The unique mechanic and his similarities to Charizard (both being dragons) helped make Ridley an easy late addition to make.
Everything else in the CSS follows the mold carefully. Shulk is still grouped with the third party characters for the sake of rudimentary roster placement.