Maybe it would be a nice idea to put certain things into a folder. Like all of the .txt files, usermap files and such. Looks more clear.

Can you give some specific examples

Userdata
Warps
Txt (containing all .txt files)
Csv (containing usermap.csv and items.csv)
config.yml
kits.yml
jail.yml
spawn.yml
worth.yml

Too much work when barely anyone looks at the Essentials folder. imo.

I don't see what this achieves, other then making it slightly harder to find files?

I don't see why it would become slightly harder to find files? Currently there are a lot of files in the directory making it look messy. Ofcourse, I don't know how much work it would be.

Because it's an extra folder to navigate from either a command line or file manager.

This would also result in inconsistencies between EssentialsX and the original Essentials documentation, which while it might not seem like an issue, it creates unnecessary confusion for new users.

I don't think this is necessary.