A consistent system settings app that actually handles all configs without requireing manual editing of config files.
Which DE? With KDE I don’t think I’ve ever had to edit a config file. I do recall that being an issue with Gnome; it’s been years since I’ve used it though.
On KDE, if you want NumLock to start on at the login screen, you need to edit a file.
Also, to remap mouse side buttons, you need to either mess with a config file or install something like Input Remapper.