Why? The rosters only going to get bigger, and quite frankly I don't think Sakurai would be keen on adding clones to the roster. Even if the current clones remain as-is, they'll be drowned out by a whole bunch of non-clone newcomers.
Because the larger the roster, the more difficult it becomes to balance.
One more thing to add, even in story-telling paradoxical "clone" characters are boring and uninspired.
>Evil Goku
>Shadow the Hedgehog
>Mecha Sonic
>Waluigi
>Cell
The Dark version of the Hero who is just evil to be evil is just flat out lame. Imagine if there was in "Evil" King Arthur in the Arthurian Tales, how lame would that be? Paradoxes and contrasts are best reflected in characters that are opposite to the hero in nature and appearance. Not the same thing but redone. The Hero is honest, handsome and heroic? Well, the paradox character resonates by being the exact opposite, gruesome, cunning, vindictive, ect.. The more differences there are the better. Look at Mickey and Bluno, they're polar opposites, and thus they work very well.
The only time I've ever seen a "clone" figure be interesting was in Bleach with Hollow Ichigo, and that was simply because his personality was so radically different, that it was ok, not to the mention the psychological aspect of it being a mental manifestation if Ichigo's instinct (that of course was ruined in typical Kubo fashion as the series progressed).
It's the same idea in other media. Much more thought is put by a writer when he thinks up a character than can contrast the Protagonist's figures, than by one that says: "Ok, now I take Sonic, and I color him Purple, he's the Evil Sonic, with the same abilities, but a DARK personality, ORIGINAL CONTENT DO NOT STEAL." Anyone can do that, as evidenced by ****ty fanfics. Read Heart of Darkness and contrast how Kurtz is a paradox of Marlow. Or Frankenstein and compare the Dr. to the Monster, THAT's a paradox done right. Anime, Manga and Vidya do it too sometimes, but these days it's hard to come by. Good examples would be Guts and Griffith in Berserk, or Kenshin and Shishio in Ruroni Kenshin, Light and L in Death Note, Dr. Tenma and Johan in Monster, etc...
In fighting games it's the same thing. One developer puts a lot of thought into making a character, even if there are similarities.
Noel to Mu-12
Carl to Relius
Sol to Order Sol
Ky to Robo Ky
Sagat to Adon
etc...
And the other just copy pastes abilities from one on to the other, adds a couple differences and calls it a day. Tell me, which one put more effort in? Which one is of better quality?
Ryu and Ken made sense in context BECAUSE they were supposed to be identical recolors of the same characters, but the Capcom went out of their way to make them different. It's the same Scenario as the Super Mario Bros. in SMB and Smash64. But had SF been conceived in recent times, and we got Ryu and Ken as clone-esque characters I would have been well opposed to it.