The actual reason is that one of the big flaws of S3K's setup is that super forms removed character variety. When you go super in S3K, all characters need to go fast while collecting rings. It's preferred to avoid using your abilities as much as possible because they slow you down. This basically makes S3K have four characters: Sonic, Tails, Knuckles and Super. When you play all-emerald runs you initially start with unique character abilities but then end up with everything the same by the end of the run. This ruins the whole fun of having unique characters to begin with.
You'll noticed that Sonic and Metal's SRB2 toolkit overlap with a core theme: going fast. Super does not disrupt that gameplay because you were likely already trying to do that, thus it enhances the toolkit they already had and gives them a new way to do what they were already doing. The other characters in the game are not designed around going fast. They have abilities that encourage other behavior, and if we gave them super then we'd just have the same issue S3K has where everyone becomes the same once you get the emeralds.
Something we've occasionally discussed in the past is giving the other characters completely different perks for getting all the emeralds, but this isn't a high priority so even if we decide we want to do that, it'd be a long time before we could implement it. In the meantime, though, I really don't want to ruin the character variety SRB2 has, and thus, I strongly disagree with the idea of adding super to other characters in vanilla. If you'd like to mess around with super as other characters, you'll need to mod the game.