I can appreciate wanting to keep my way over some other “things” way. Totally understand. I also get frustrated with reasons like “the computer says I can’t do that” or similar statements.
After many years dealing with technology I’ve learned you either make your own effort or match other folks effort. In the former, you get things your way. In the later, you get things their way. You just have to find a balance there somewhere. Maybe Emby or Jellyfin might be closer to your way than Plex.
I think that’s fair to say but will point out that the majority of users are not anime fans and anime is definitely an exception to the rule in the TV ripping\media community. Just look at how much codec work was necessary in the past to watch stuff… individual codecs like XVID and custom fonts for subtitle support up to codec packs like CCCP and K-Lite before MPC and VLC came along with bundled codecs but still not “easy” to deal with really… and all could be based around personal file\folder structure.
Anime is just an oddball in this realm and it’s hard for software to account for it while still working well for the majority of other users that don’t need special attention to make things work. 
That being said, anime is popular and there are plugins you can try that will help Plex match anime… it’s just a different effort for you and it’s not “official” so Plex can’t help you with it. I think the scanner is HAMA and you can find stuff about it here: [Rel] HTTP Anidb Metadata Agent (HAMA)
It might be worth checking out. Good luck!
