needless sandobxing (by default flatpaks can access your filesystem but not mounted folders, how is that secure and not jist inconvenient?)
yet another application manager not even well integrated into operating systems (linux mint doesn’t update flatpaks by default)
applications are usually not updated very often, not sure if that’s a systemic problem or just laziness
application X that is 50MB stabdalone requires 2GB to install and takes 3GB of space because it requires the entirety of gnome libraries. Application Y also requires 3GB because they use KDE or another version of gnome