The problem is with giving custom characters super forms, is that every character and their dog had a super form. As a result, well, turning super was not special anymore. That and there was a crackdown on overpowered wads that were starting to get rather annoying, I imagine the decision to remove the ability for character wads to turn super in single player/coop was also influenced by this.
Although, back when 2.0 was released, there was a discussion on the forums about a different system that would give people creating character wads more control without enabling them to create overpowered characters. For example, one idea suggested, was that if the player wanted a super peel out (like in Sonic CD) they would have to give up the Spindash. Or raising the max speed of a character would reduce the acceleration. Although, this was at least half a year ago now, and I don't know if any progress was ever made on this.