Jellyfin's worst aspect is the opinionated file structure. You have to set up folders the way it wants, and then the resulting UI browser is what-you-see-is-what-you-get. Pretty sure it's done this way for automated metadata discovery.
Ideally, this would be designed in two parts: separate the file structure from the metadata discovery mechanism.
I personally want a file structure managed by the OS. Let me make folders and nested subfolders to whatever structure I prefer.
Then make the metadata discovery slightly more manual. Click a media file, click a hypothetical "add metadata" button, and then a simple search box with "is this your movie?" and click apply to import metadata from a search result. easy peasy.
The UI is clearly meant to resemble a typical media app but falls short if the end user prefers, for example, foobar2000's UI.
Yeah that's the Number 1 issue I have with Jellyfin.
It seems to be tolerating whatever semi-organized structure I give it until it just faceplants on some specific show and I have to tediously reorganize the directory structure/names and manual refresh until the metadata lines up correctly.
I like that I don't feel I'm about to be rugpulled on Jellyfin and the client is pretty solid for me but the library scanning is pretty aggravating at times.
I'm OK with structuring file layouts however it wants. I'm even OK with giving Jellyfin a whole directory tree full of symlinks that are organized exactly how it desires, and then automating its ongoing maintenance.
The thing I'm not OK with about Jellyfin is that the common answer for remote access involves setting up a reverse proxy or a VPN or some other darned thing that I will never be able to talk my mom into configuring her Roku to be able to use.