This isn't fair to Mystic. I hate that I have to defend him but when someone is deemed odious to a community's culture it's important that people remember his character accurately, not turn him into a punching bag for every outstanding slice of beef. He was an individual who grew rotten and entrenched over time and I couldn't stand by the end of his tenure, but he was stubborn, not stupid.
He knew, objectively, that Knuckles turned Super in his debut experience. What marked his approach apart from others on this topic was that he viewed that as a thematic choice driven how focused Sonic 3&K was on exploring Super power and Emerald lore - Knuckles was Sonic's rival and could do it, Mecha Sonic was the dark mirror, etc.
Since Knuckles was not the rival of SRB2 (Metal Sonic would be a much likelier candidate), and the entire game was less plot-focused, almost like a 3D version of Sonic 2, there was no pressing need for Knuckles to be able to turn super - which was good for him too, because one of his core beliefs was that the characters should be different from one another, and he couldn't conceptualise a Super Knuckles that mechanically gelled with the changes made to him over time.
As you can see, to him, the question of "should Knuckles turn super" was not a question of following an existing power checklist. He was phenomenally disinterested in the concept, and I think it's to some degree a generational thing (he was in his mid thirties when we last talked properly). Keeping an encyclopediac running tally of a technicolour animal's special abilities is a mindset that has become vastly overrepresented in the population thanks to the rise of fan wikis, Death Battles, and nerd culture in general, and I can't say it's a completely meritless endeavour to reject this way of thinking and instead think about what any particular game needs from a design perspective.
The negatives, then, are twofold - that it's a wedge issue that will make you incredibly unpopular with people who DO hold this mindset, and that if you are chronically incapable of defending your decision without resorting to shutting down discussion or other toxic responses your game design decisions will not be respected as you'd like.
what am i even doing i've hated mystic for a long-ass time why am i defending him at 5am