Jellyfin seems to struggle a bit with my anime library when the files don't follow a typical western TV show structure, but I'm otherwise very happy with it!
The one issue I've had is with Danganronpa but that's because the backing service for data (TheMovieDB) wants to insist that DR3 Future arc is part of DR1 and not related to DR3 Despair arc.
[group] anime name - 01 [fileinfo] [crc32].mkv
This becomes problematic when you have shows like New Game, where the first is stylized as NEW GAME! and the second season is NEW GAME!!. Jellyfin shows them both as the first season of the anime, where as Plex with the Hama TV scanner can distinguish between them.