@element For the sake of this discussion I glanced over the Arch Wiki page about Flatpak again. Specifically the troubleshooting section.
"There is no ideal way to apply system themes in flatpak apps"
"There is no single standard to set the cursor properly."
I find this unacceptable. The response to "Flatpak is not the future" is only giving me more reasons to avoid Flatpak, as it fails to defend the original arguments.
However, I do believe Flatpak can be a great way of distributing software, if - and only if - all apps and system components are Flatpaks. But at this point you might as well consider Flatpak it's own Linux distribution.
To me, the only use of Flatpak in its current state is more like an emulator. It's not really emulating anything, but it enables some applications to run that wouldn't otherwise run on the system, which is a common use case of emulators.