This is a little late, but I think it was Sonic who replaced Mewtwo. This may seem strange to some, but there's evidence that Mewtwo (along with Roy) was actually in Brawl at one point. Among the scraps of data for Mewtwo, he even has a Classic pre-fight screen. That seems to be a pretty good indicator that he was actually in.
(Speculation from here on out)
Then, last-minute, Sonic and Wolf got added to the roster. (There is also evidence that Wolf was the last character to be added into the game). During the time used to add those two, I suspect that Sakurai would have opened up the clone factory, producing the rest of the forbidden seven (Dr. Mario, Toon Zelda/Toon Sheik, Dixie). But since there was no time to make these clones, Pokemon had more CSS slots than Mario, and a cut needed to be made for political reasons. Mewtwo got the axe.
This isn't a perfect theory, but I think it's fairly probable.
Anywho, what do people think of a Tetra/Toon Zelda's possibility in SSB4? (Braces for Wizzerd attack)
I think it's possible (seeing as Toon Zelda was a cut character in Brawl, Sakurai clearly has his eye on her), but I doubt she'd get in before Tingle.