And thereby refuting the fan claims that only hedgehogs can go super--even though they still say that now. Even after Knuckles and Tails went super. They say that Knuckles can only go super because of his connection to the Master Emerald. Also, Tails can only go super because after the trouble of getting 14 Emeralds, they had to give the player something. I don't really agree myself.
Well, there's two schools of thought that you can utilize, if you really want to side with the notion of "hedgehogs go super only".
For one, the main reason that leads to the notion of why the Super forms of Tails and Knux existed in S&K3, and furthermore, the Hyper Forms for everyone (including Sonic) in the same game, was more or less a "gameplay bonus", rather than being a "canonical" thing.
In short, like you suggest in your second-to-last, it was more of a thing of giving the player something fun to strive for, rather than really having an impact on what to expect in the series from that point onward.
Secondly, canonically, only Super/Hyper Sonic was the one who was able to take on Eggman in the final fight of S3&K's story line. Meanwhile, you were forced as Knux to to deal with (Super) Mecha Sonic without such a perk (all the more reason why I consider Knux more manly than Sonic!
). And Tails' "storyline", of course, is tied to Sonic's. Some how, the kitsune makes it back to Earth in just enough time to fire up the Tornado, so to help Sonic on re-entry.
But in any case, notice how even Hyper Sonic and the "Super Emeralds" have yet to make any re-appearance in the series, which probably just goes to show that they, like the other frivolous forms, were bonuses, rather than something we should come to expect as "canon" for the series. Even that moment when Tails and Knux were flying alongside Sonic in "Heroes" wasn't anything beyond the notion of how Sonic was able to some how generate some sort of "forcefield" to allow them to fight with him. So, as of right now, there's nothing that points to the notion that any one besides a male hedgehog (sorry, Amy), is able to use the powers of the Chaos Emeralds in such a way. I blame the whole thing of the Sonic series doing more to ride DBZ's lap about this whole thing (Saiyajins = Hedgehogs), as time went on.