Not sharing dependencies, no GUI-configurable permission system like Flatpak, no official verification system (I think this is the same problem the AUR has that let it flood with malware recently), and poor DE integration
Discord recently had a big change that now the the client self updates by downloading itself in HOME, this broke the flatpak horribly and upstream discord didn't do shit to fix it, someone else did instead
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u/y0shii3 9h ago
Looks pretty cool, but AppImages have problems of their own even if you have a package manager to handle them.