In the speedruns for Mega Man Arena, one variable we include is version number. With each new major version, new characters and bosses are added, so for our category of Marathon%, where you beat all bosses with all characters, obviously the older versions will be faster. However, we want to obsolete the old marathon run because it's impossible to beat and no longer representative of the game. I can't find any setting to obsolete runs by version though. Is there any way to obsolete the run without completely removing it?

There is no way to force a specific variable value to always be obsolete. Your best option would be to move these runs on the older versions into a separate category or subcategory.

One way to do that is to rename "Marathon%" to "Marathon% (Pre-whatever)" and make it Misc. Then just create a new category called "Marathon%" which will be for all up-to-date characters. That way, you don't delete anything and people can still check out the older runs.