Wario does represent WarioWare so I'll give him a pass. But Yoshi on the other hand is really more of a Mario character than anything, regardless of what Smash Bros. Says.
It's not regardless of what Smash Bros says because Smash Bros is the series we're discussing. Regardless of what you personally consider Yoshi to represent, according to SSB the Yoshi series is as seperate from Mario as Mother or Fire Emblem.
In terms of physical slots on the roster no series has ever eclipsed Mario, which is a perfectly astute observation (although "Mario Theory" really bugs me as a name for it). Even Pokemon, with its "six" characters in Brawl, still stood at four slots alongside Mario and Zelda. With the inclusion of Rosalina and the seperation of Zelda and Sheik, Mario and LoZ now each have five slots if we assume Ganondorf is returning. Taking this further, Pokemon also has five slots if we assume Jigglypuff is returning. That's a proportional increase of one slot each for the main three series. This observation by itself, without any extrapolation beyond Ganon and Jiggly, is accurate.
As for the question at hand, it is impossible for Ghirahim to replace Ganondorf.