I like to keep my files and folders very well organized, which sometimes means I have some files that are nested pretty deeply.
This will allow for folder structures like the below to be scanned and still have Plex use the file’s name to find relevant metadata.
universe/
phase-1/
1/movie (year).mkv
2/another movie (year).mkv
phase-2
3/later-movie (year).mkv
4/even-later-movie (year).mkv
I assume you’re aware of the Plex media naming recommendations? That’s the gold standard for “very well organized”, at least for the purpose of working with Plex.
There’s no other objective standard for “very well organized”. Yours looks like lunacy to me, but the best thing about opinions is that I don’t have to smell yours. 
Assuming you’re using the Plex Movie agent, you could try embedding the IMDB/TMDB ids into your file and directory names. It gives a very strong hint to the agent.
See the link above:
I haven’t tested this. I don’t recommend it. But I’m curious if it works :
mcu/
phase-1/
1 {imdb-tt0371746}/iron man (2008) {imdb-tt0371746}.mkv
2 {imdb-tt0800080}/the incredible hulk (2008) {imdb-tt0800080}.mkv
But … seriously, don’t do this. Plex is opinionated about file naming and organization, and you’re swimming against the current. It’s easier to work with the system than against it.
Displaying things in groups like this is a job for Collections or Playlists within Plex, not at the filesystem level.
My movies are all named by “Title (year)”, which should be more than enough. I’m aware of the recs and they don’t say anything against having multiple subfolders.
While I understand that Collections and Playlists exist, I also want to organize my files such that they make sense should I ever wish to port them to another service or if I end up watching my files through a basic file system.
Having the option for deep recursive search is a small ask. Other services, like Kodi, do this and there’s no reason Plex shouldn’t do it. As long as it’s optional, it will not affect most users. Furthermore, it makes the service more appealing, useful, and flexible to more users.
Lastly, I do not appreciate the unnecessary snark about my feature request being lunacy or smelling. There’s no need for that at all. And since deep recursive search is an option in other media services, it is clearly neither lunacy nor smelly.
Your naming system will already work, with a small modification: Add one more folder level, being the movie name and year, in which you place the movie file. Using (part of) your example above:
universe/
phase-1/
1/
movie (year)/
movie (year).mkv
2/
another movie (year)/
another movie (year).mkv
Once you move beyond the structure (or lack of) of dumping all of your movies into your library’s root folder, Plex uses the folder in which the file lives to determine the movie name (not just the file name itself, that is still important particularly if you have extras). So, once you have a tiered folder structure, the last folder name must be that of the movie. That’s the reason for the behavior you described in your other thread.
I could make some educated guesses as to why the scanner works this way, and they’d mostly have to do with how Plex allows you to organize movie extras.
2021 clean-up: as pointed out above, this will already work if the actual movie files are in a dedicated folder for that movie (named according to the Plex naming schema)
