If it means more characters, I'll gladly take more clones. I wouldn't care if Dr. Mario was de-cloned or not. I'd take him right away regardless.
Even Pichu, who is the only clone that bothered me(Dr. Mario is arguably Mario as is, and as noted by Miyamoto, he might be an entirely different universe Mario, and not like the current one, so technically different people) at all, I'd want back. He's the hardest to change, though, but it's possible.(Zap Cannon for Final Smash perhaps?)
I'd gladly see Roy back even if it he didn't get de-cloned as well. I admit that Lucas feels like a spiritual successor to Mewtwo in playstyle(to an extent, B moves not so much as some fairly similar A moves in design. I know they still play differently, but the Jump is still about the same, and the whole various elemental/almost magical attacks reminds me of him)
I still would like to see Ganondorf further de-cloned, something closer to what Luigi is now. Keep the Up B and Forward B, give me his Energy Balls for B(hot, right?), and Down B probably his Earthquake. Or fully new moves, with the ability to switch versions via the D-Pad similar to Samus being able to change to Zero Suit. Alternatively, X or Y could be a "Change Moveset" that gives you either new B moves, new A moves, or both.