I used to have the same opinion, up until I get how things work with Flatpak apps better.
It was so confusing at first as to why saved files sometimes don't appear in the right directory. Then I learned about Flatseal, which I used in initial setup and whenever some things don't work right. It gives me a nice and simple GUI way of managing permissions, which I like as a layman.
Theming was confusing at first. The best I could do initially was setting env variable on Flatseal with GTK_THEME=Adwaita:dark, until it clicked to me that the config folder inside ./var/app/flatpak.app.name/ folders is the config folder they access instead of ~/.config so I could just copy-paste the gtk-3.0 (or 2.0, 4.0, or all of them) folder in ~/.config to get theming to work.
The only thing that I haven't figured out yet is Native Host Messaging or whatever it's called, that's needed for connecting with things like Global Menu and Plasma/GNOME Integration extensions on browsers.
It was a hassle at first, but like learning Linux, I just learn it bit by bit. And now I like it because at least there's an easy way for me to find and get the apps I want. It's easier to deal with than Snap and AppImage for me now. Hell, my experience dealing with dependency issues with CrossOver on Arch made me wish they have a Flatpak so I don't have to deal with it.