My experience with Flatpaks has been so stable and hassle-free that it motivated me to switch to Fedora Silverblue.
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Hell yes! Feeling futuristic.
almost all my apps are flatpaks
I like them for convenience, I don't like them for customability, possibly just because I don't know enough about them.
That is a good point I have not encountered too often. I don't tend to customize the programs I use. I tend to just learn the defaults for that program.
Anyways, people keep recommending FlatSeal, which is a graphical way to customize Flatpak permissions, so that may be helpful to you.
When I first used it it felt like they were usually out of date or missing. But nowadays It seems like I can find like 90% of the apps I use as flatpaks, leaving packages mainly for backend and terminal stuff.
Unless they come up with something else that is not "Windowsfying" Linux with one-click installs... then nah, no thanks.