It is really quite simple.

Flatpaks (and Snaps, and Appimages and Docker containers for that matter) are essentially designed for app developers who grew tired of distro maintainers demands to fix certain things about their build systems and their applications that broke when their apps were used on distros other than the exact distro and version the developer was using. They are designed to take a "kill the messenger" approach to the problem and now people are wondering why the work that the distro maintainers did before doesn't get done any more.

The default permissions for each app are up to the package maintainer. If something seems odd about a package, complain there.

Well I hate to disagree with all the doomers here, but I don't think flatpaks are the devil. Flatpaks are as good as the person shipping them, there are not many flatpaks that actually have official dev support so a lot of these programs are packaged by volunteers in their spare time. So no, they may not have the best default settings.

That said, I run flatpaks almost exclusively on Kinoite I've never had an issue with flatpak theming or my cursor changing. Some applications are very obviously made for GNOME or KDE explicitly but flatpak doesn't have anything to do with that. Of course if you are running a WM rice or something with very specific theming then that's another story. You can customize a Linux desktop in countless ways, you can't really expect these applications to keep up with that by default (flatpak or not). It's the same concept as something like Discord or Steam, it will look the same for everybody but you can theme it if you put some effort in.

IDEs are another issue, the whole concept of an IDE is antithetical to a sandbox in the first place so it's simply not a very good use case of flatpak. Flatpak isn't a one-size-fits-all solution, that's why even the Fedora immutable desktops give you additional options like rpm-ostree, podman, buildah and toolbox.

That theme situation is a bit odd, there should be better documentation about that.

The very concept of them is that they bring along basically everything but the kernel - all their library dependencies, all their config, everything. So they're 'reliable' and 'easy to start', but also bloated, slow to start, resource hungry, don't depend on system libraries that can be updated independently, and as you see, look like crap. Working as intended, nothing to see here.

It is curious cause I also had a very bad experience with flatpaks, a lot programs just won't work and the terminal integration... is just bad, really bad.

I think the container idea is not for everything and ppl should stop pretending that is marvelous. It actually work for most apps after a big improvement in usability but not for everything.

Themes, cursors being inconsistent (needs to be fixed manually with flatpak --user override

I haven't had this issue in about 6 months.

IDE’s are unusable without extensions

Yeah, IDE integration is kinda bad. Use containers instead.

Next problem please?

It's pretty simple: RedHat/Gnome developers don't believe in theming and that you should stick with the default theme and suck it up.

They even made a whole website about it: https://stopthemingmy.app/

Some apps automatically pick up your theme some don't. For these I give the specific app access to my theme folder with a :ro at the end of the path.

IDEs should work ootb. If some extension doesn't work, maybe it's because of poor support for Flatpak. 9/10 times you'll find the issue is that app is calling the traditional /usr/bin path etc. when Flatpak installations use different paths.

I can't stand any of the new packages except appimage, flats & and snaps just cop outs

because they dont exist to make it esier for users.