I usually try to stay out of the whole snap vs flatpak discussion. Although I am just really confused as to why flatpak just does not seem to care about usability. You're trying to create a universal packaging format I would think the point of it is that a user can just install an app and after reviewing permissions it should "just work".
There are so many issues that yes, have simple solutions, but why are these issues here in the first place.
These are the issues that I have encountered that annoy me:
Themes, cursors being inconsistent (needs to be fixed manually with flatpak --user override
IDE's are unusable without extensions
At least snap provides an option --classic to make the app work. Please explain to me why flatpak just evidently refuses to take this same approach.
Tl;dr it's likely that some of your hardware isn't well supported in Linux or have vendors downright hostile to open source (fuck you, Broadcom and Nvidia) and causes you weird issues that almost always get fixed by the community but may not always work "out of the box"
I've been in Linux since 2008 and have asked this question in many ways over the years. To get a real answer I'd dig more into the errors you're encountering. I think that a lot of the "simple fixes" you mention are simply options that some hardware configurations need and some don't.
Flatpak and Linux in general deal with the same huge task as Windows, which is "support any hardware configuration with one universal solution". While Windows is given every advantages by cooperative hardware vendors releasing official drivers, Linux is mostly supported by open source reverse engineered drivers.
This means that no "universal" system is likely to work all the time in every case, but that's ok because it's all open source and the community finds a way.
You mentioned themes and some graphical packages, do you have an Nvidia GPU? I never had anything but trouble on Linux with them.
It has nothing to do with my hardware. Like I said fixing the theme was done with a simple command that basically mapped my user .icons folder to the flatpak one. My point is just that why isn't this done automatically. Why isn't there a system in place that will deal with this.
If it bothers you that much, write one. 85% of Linux was constructed by frustrated nerds deciding to write their own solution to a problem they found. There is no parent company to complain to, just fix it yourself and distribute the solution. Else, you'll need to wait for someone else to do exactly that.
I can't say with any specifics but flatpaks are sandboxed on purpose, when you override something you're giving it more (or less) permissions than the developer thought they'd need. "Automatically giving permissions the developer didn't think they'd need" seems like a crazy thing to try to automate, no?
Check out Flatseal if you haven't already. It's a GUI for flatpak permissions. Might make your life easier in the future.
Yeah I understand the reason why it is the way it is. I think it should be simplified. Just a pop-up box asking the user if it's ok if flatpak gains Access to path x. That's what I have in my mind. Maybe with time it will improve.
I can feel your anger and frustration in your messages here and I just wanted to say I think your idea is fantastic and you have an ally here to fight with you.
It was mostly rhetorical. There's no way to know that you want the application to have extra access to some folder needed for your theme. That's the exact kind of thing that would be better handled on a user-input level. You applied your theme, you notice that it is broken with the app, you apply the new expanded permissions to get it to work with your theme.