Yeah, slow app launch for one thing. Lack of DE integration for another. Flatpak apps are so completely foreign elements in the distros I’ve used that I have no inclination to use them.
And the few times I’ve had to use on, it’s so bloated with redundant dependencies. I understand that flatpak apps will share dependencies within their ecosystem(?) but since they’re the exception to the rule on my system it never becomes a benefit.
Besides, as is OP’s point — I have the entirety of the AUR at my fingertips. Why would I bother with anything else?