I have been thinking about it (ever since you originally mentioned the problem). We already have a (rather ugly) $1Q and $2Q variant to force the recording as movie or tvshow. So, it's possible to add variants for using additional subdirectories, but the question is how to make it not even more confusing/ugly, though I'm guessing it will end up being just a "$3Q" and hide our heads in shame...
I'm slightly against adding a new top-level tag "$Z" (or whatever) just because I don't want to use up all the remaining letters for someone else's new features.
So $3q would be "tvmovies/Title (YYYY)/Title (YYYY).ext" and "tvshows/Title/Season XX/Title - SXXEYY - Subtitle.ext".
But, what if the show doesn't have a season? Or no season and no episode? (Currently we just ignore that bit in the filename IIRC). My OTA also has some that have a season but no episode.
I've no time to do it this weekend, but if we can think of a good think for no season, episode, or season&episode then I'll try next week.