- fullscreen mode (dark mode / theme preferably, even if I would have to make it manually somehow)
- option to navigate my drive or external drive
- xbox controller support
- subtitles support
I'm a bit confused as to why Kodi isn't working fine for you when it comes to all of this.
I use it on an old laptop specifically for media and all that stuff works perfectly for me, although, admittedly, I do sometimes find that Kodi can initially be somewhat unintuitive (I also had issues when I first set it up, and I think the official wiki is basically required reading at this point).
Either way, no idea why you're finding issues with those features.
It should be fullscreen by default, but if it's not, (I think?) there should be a fullscreen button somewhere in the top left of the home page if you're using the default skin.
There are dozens of skins/themes you can install, some of which are pretty dark by default.
I personally disable the entire library scanning thing and just browse my external drive because I prefer doing that due to my own organisation of media.
Multiple controls are natively supported, including most game controllers like Xbox (provided the kernel has the drivers, and if you're using Windows it absolutely does), and you can also use your smartphone/tablet as a remote control, if you'd like.
Fully supports most popular subtitle formats, as well.
The reason it's messing with your files is because of the way sources can be set up. Don't add anything to a specific "media library" and disable all media scraping add-ons.
You can just add your drive (or specific directory) as a basic source and browse it via Kodi's native file manager that way. You'll still get thumbnails and basic metadata info, but nothing else (which is perfect for me, personally).
I'm not at my machine right now, so I can't really give instructions on that specifically, but for any other stuff, the rest of the Kodi wiki is fairly detailed.
Again, I also think it's sometimes a bit unintuitive, but once you sort it out, it can just be left alone to do its thing and shouldn't bother you with anything you don't want. For me, I use it as a pretty basic media player, just using a few extra features here and there, but not really as a library management tool like most other people do.
I would install the backup add-on, though, so you don't have to go through the whole setup again if you happen to lose the configuration or accidentally enable features you might not want.