Flatpak often trips over its own feet with their attempt to sandbox apps, they hamstring their own capabilities by not having the necessary file system or device permissions. Attempting to use the Flatpak version of Steam for example, it couldn’t see my games library because it basically had no file permissions. Yes, this is the packager’s fault and not Flatpak as a whole, but why do so many packagers fuck this up?
Flatpaks also install in /var for some reason rather than like /usr or somewhere that makes sense, and they have commands like “flatpak run com.steam.Steam” or whatever rather than just “steam” so a lot of pre-existing machinery fails if you’re using the flatpak versions. Flatpak essentially breaks any case where you pipe data into or out of an app. A recent example I ran into is trying to use MakeMKV as a blu-ray decoder for VLC. A major selling point of Flatpak is it can’t do that.
I had a higher opinion of Flatpak when I entirely ran Mint Cinnamon and it was an additional software source. Fedora treats Flatpak as the main source of GUI apps, a lot of them aren’t available as .rpms and it’s worse.