A lot of the problems users have with flatpak come down to applications that know nothing about flatpak doing things like they would on the host. When apps are designed to work with flatpak, they work really well.
@brainblasted there are some limitations stiil like when flatpak apps need to interact with apps in the host system. the exanple that comes to mind is gnome-contacts; gnome-caledar flatpak versions needing to interact with evoluntion-data-server on the host system. if the versions are too far off it wont work because api is not compatible. gnome-boxes has issues with forwarding from usb ports. because of that smartcard readers like nitrkeys dont work with gnome-boxes.
@brainblasted if a flatpak app is self contained; it works ok. but the moment it needs to interact with apps in the host system problems can happen. Flatpak can have it's uses. But it is not a silver bullet. It also has limitations