Look, I'm a huge Metroid fan too, but the fact of the matter is, it's very easy to see Sakurai's point. In all but the first Metroid game, Ridley has been portrayed as an imposing, menacing character. It's been a consistent trait for him and the point is that as Samus, you have always felt tiny compared to this large, dragon like character. Taking this away from him would be taking a huge part of what makes the character unique. It's not simple enough to "do a Charizard but make him a lil' bigger," it'd be like making Gohma from Zelda a playable character, but making him Bowser's size. Yes, technically you could do it, but then it wouldn't feel the same.
And yes, I get the whole "scale is relative" argument, but let's be honest; Bowser's height and size vary wildly from game to game. Yes he's always bigger than Mario, and sometimes he's massive, but other times, he's simply scaled just a tad bigger than Mario himself. Likewise, yes Olimar is technically supposed to be tiny and miniscule, but again, from the framework of the Pikmin game the sense of scale comes only after you realize that you're tiny very intuitively by the things you start to collect and see in the game. In that sense, the game never makes you ever feel tiny or insignificant, but rather that everything ELSE in the world you're interacting with is massively oversized. By that same token and going back to my original point, wouldn't it feel strange if the Bulborbs in Smash Run were "scaled accurately" and made to be the same size or smaller than the playable characters?
As for Ganondorf... yes he's a modified clone at this point of Falcon. But should you really use this as precedent to put in a half-assed Charizard-Ridley character? Melee was a game that Nintendo wanted to get out quickly for the 2001 Holiday season, and there's no doubt in my mind that if Sakurai had more time for that game, Ganondorf probably would've ended up more unique. Unfortunately he's put in between a rock and a hard place in terms of revising or changing and it's pretty clear that he's erred on the side of consistency.
To me, it seems that a lot of the argument is for another Metroid rep which I can understand. It is one of Nintendo's premiere franchises, and it should have a good rep. Unfortunately, there really ISN'T a good rep outside of Samus for Smash. Most of the main boss characters (like Kraid, or Phantoon etc) really wouldn't work unless Sakurai wanted to use some completely forgettable bounty hunters from Hunters or Prime 3, or some generic space marine from Other M. Dark Samus probably would be the closest but she still remains in AT limbo for now. So yes, I understand where the enthusiasm is coming from as Ridley's probably the closest thing to fitting but even then, it really isn't a clean fit for the reasons I outlined above.
Just looking at this grass-roots campaign for Ridley that's seemed to come up more prominently for Smash 4, it's very strange to me. Even the whole revisionist theory of "oh they were cheering for Ridley not Samus" during the E3 2001 debut of the game is just very funny to me, considering I remember the build up to E3 2001 and the anticipation of ANYTHING Metroid... not Ridley.
Maybe if the next Metroid game comes up with a kick-ass antagonist that can give Samus a run for her money, we'll finally get a rep. But until then, I feel like trying to shoe-horn Ridley into Smash is fitting a round peg into a square hole.