I have a WebDav server that contains some movies and shows. I use Infuse on Apple stuff and NOVA Video Player on Android to watch these. The directory is not organized, file names aren't manually adjusted, and the movies and shows are mixed together. Yet, both of these programs are able to index recursively, get metadata, create a library and let me watch my media without issues.
Kodi, on the other hand, seems to be unable to index nested directories, requires you to tell it what type of media is in the individual directories and cannot identify anything correctly unless I go and manually rename directories/files. It also is exclusive for TV usage and not very suitable for desktop.
So, are there alternative programs to Kodi, ideally better suited to desktop usage or extensions I can install to make it work properly?
Just organize your library properly and pretty much every software will manage it better. There are options for organizing and renaming them mostly automatically, like EastTAG or filebot. Some people use Sonarr and Radarr to organize shows and movies, but those are probably overkill for you. The various *arrs will be more useful if you're consuming new media through a server hosting Plex or Jellyfin. Kodi is also a waste if the library isn't already meticulously organized and you don't need a 10 foot interface.
If you're only consuming on desktop and you insist on being disorganized, then why even bother with anything other than VLC? It runs on Linux, Windows, iOS, and Android.
People keep talking about needing to "organize your library" but what do you mean by that? Is metadata tagging sufficient? Or does Kodi care about filenames and directory structure?