The problem is that neither the Cinematic Titanic nor the Rifftrax groups own the MST3K IP.
(Also, since MST3K became Kind Of A Thing, nobody was willing to license their movies anymore without wanting exorbitant fees because hey, that thing is actually making some money.)
Going from a puppet show you and your friends tossed together on cable access to one of the most influential comedy shows of a generation is a Hell of a thing to do.