Command line software does show up in CLI, just not by its short name. You have to use the fully qualified app name - com.xyz.whatever. You can make an alias if you want.
> Even worse, while there is an option to install things in the user's directory only (so i can make a separate user to try some things that i can easily delete later) not everything installs with that options and wants root access to pollute the rest of my system.
Are you talking about flatpak install --user ? Yes youre right some apps might not work with it but how is that any worse than traditional packaging.
Flatpak isn't perfect and I prefer distro packaging over everything else but it isn't feasable to have distro packaging for everything - not with the strict packaging rules most distros have atleast.
But out of snap, appimage and flatpak I'd go with Flatpak.