Would a run done on the original version be accepted now? If not, shouldn't there be sub-categories for "Legacy patch" and "Current patch"? There are some runs here that were played on older versions from years ago. Same goes for the Wii U version.
https://www.ssbwiki.com/List_of_updates_(SSB4-3DS) Glitches, character balancing, and AI improvements.
I'm not a mod so I cannot make any executive decisions obviously but I don't think those changes warrant sub categories.
Other games get categories for old patches, like Cuphead. But I see where you're coming from, since this game doesn't have a very big speedrunning scene to begin with. The rules should at least say "Play on the current patch" if the mods don't find much reason to differentiate.
Unless a glitch in a version (exclusive to that version) that saves a significant amount of time is found then it makes sense. But @SoopaPhastMan your idea about the rules makes sense
Just do runs on the most current patch
