In a surprise move, Ubuntu developers have agreed to stop shipping Flatpak, preinstalled Flatpak apps, and any plugins needed to install Flatpak apps through a GUI software tool in the default package set across all eight of Ubuntu’s official flavors, as of the upcoming Ubuntu 23.04 release.
It needs a daemon (lots of wasted resources).
You have to fiddle around in config files to allow access to files on the system instead of using something like Flatseal.
It basically only works with a store which is kind of proprietary.
Own repositories are hard to set up.
The packaging for software maintainers is harder than Flatpak’s.