Huh, anime is my primary use for jellyfin, it seems pretty fine for me with a Show/Season X/SXXEYY - whatever you want.mp4 structure.
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.