I understand, I used to manually organize my own files as well.
When I’m given the choice of user interfaces. Choosing between a file browser and something like Kodi, Plex or Jellyfin seems pretty easy, to me.
Even with the most organized file system, a file browser just isn’t a good UI for a media player interface. No user tracking (watched episodes, saving progress or playlists), for example.
That being said, everyone’s use case is different. There isn’t a “right” way, but in a multiuser environment across multiple types of devices with non-technical users it’s much easier and feature rich to simply use Kodi/Plex/Jellyfin.
Trying to setup direct access to the file system of a media server which could be accessible by Android/Apple phones, video game consoles, smart TVs as well as Linux and Windows clients would be more complex than just using a media interface and a standardized media directory structure.
I’m not trying to get you to change anything. You can organize your media however you like, I’m mostly just setting up the solution:
The solution that you’re looking for is called filebot (https://www.filebot.net/forums/viewtopic.php?t=7). In filebot you first define how you name your media and what directory structure you’d like to use. You can use it to handle ingesting new media. It will read common naming schemes used on files often shared online and re-name them into your defined directory and filename structure.
In addition, it comes with bindings already setup for the ‘plex’ format (that Kodi and Jellyfin also use) so you can, once you’ve defined a format to match your preferred directory structure, use filebot to hardlink your media library into a different Plex-compatible structure. Since you’re using hardlinks it won’t use any additional disk space.
Then you can keep your media how you always have it, have a powerful tool to handle managing that library (for example, you could define a new format and it can move the files between them) and also hardlink the files in a Plex folder structure which will let you have access to a media player interface.
If you manage any media at scale you should learn how to use filebot in any case, manually organizing a library can be tedious and take a while. Filebot is a lot faster once you learn it.