One thing that hasn’t been mentioned yet is interopability, that is, flatpak interacting with the rest of your system.
I’m not that familair with flatpak, but in my brief experience with the steam flatpak, I had trouble getting it to recognize my controllers. Steam installed through pacman (Arch’s package manager) had no such issues, on the other hand. My hunch is that this has to with flatpaks being more isolated from the rest of your system.
Im pretty sure that’s just some kind of permission issue, but it can be nice to not have to troubleshoot acces rights and the like. But this is obviously a double edged sword: more isolation may also mean more security, just at the cost of ease of interaction with other components.