One of the use cases I would like to have used Flatpak for is Visual Studio Code. Unfortunately, I found the isolation to be too onerous for developer needs. Take the Rust compiler toolchain. There's no way to access that from VSCode. There are ways to add on tools to the VSCode environment, but that feels like a kludge when I already have everything installed and set up. And if the toolchain isn't available for Flatpak, tough luck. Other features just simply don't work. I eventually switched to using the Ubuntu builds from the VSCode developers.

Edit: The Rust compiler toolchain can be added onto Flatpak because there is a packaged version of the toolchain, but it's not the host environment's version. Other tools like the fish shell might be entirely unavailable.

Take a look at this site that goes into the details of the shortcomings of Flatpak, its from 2020 but I'm sure some of this is relevant still

I don't use Flatpak much, but I rarely see issues. Sometimes I see minor things like themes not quite being right, but its never been bad enough for me to spend the time to fix it.

I suppose another downside is the need to have the base runtime packages, so it could take more disk space if each app uses a different one. In practice apps will share runtimes though.

What could be wrong with random foreign executables in your system?

As a basic end-user I have not been too happy with my experience with flatpaks. I do appreciate that I can easily setup and start using it regardless of what distro I'm using. But based on standard usage using whatever default gui "app store" frontends that usually come with distros, it tends to be significantly slower than apt, for instance, and there seems to be connection problems to the repos pretty often as well.

The main reason I don't use them is because when I move my nixos config to a new machine as far as I know you cant get them to auto install. I have to remember which ones I had installed and redo them manually.

Which is why if for some odd reason I don't want to just install from the nix pkgs repo. I use app images. I can keep them in a directory which I can just copy over to the new machine with my nixos config files.

If you have an unusual setup, it can be annoying trying to give programs permissions and sometimes it just outright doesn't work. For example, I mainly game on a laptop which has a pretty small hard drive, so I tend to put most of my games on an external hard drive. Flatpak really doesn't play well with that.

GPU drivers. It uses the Ubuntu 22.04 (LTS) userspace side of drivers. Could be incompatible with your kernel. Had all sorts of graphical weirdness with my AMD GPU with flatpak Steam.

I feel like this should be required reading for a lot of Linux users. That article is a couple years old now, but I think is even more true now than it was when it was written. Having a middleman (package maintainer) between the user and the software developer is a tremendous benefit. Maintainers enforce quality, and if you bypass them, you're going to end up with Linux as the Google Play Store (doubly so if you try and fool yourself into thinking it won't happen because "Linux is different")

Yes, the confusion that results when things don't work because of isolation.

What I find most annoying is the extra drive space required. It makes backing up and restoring my computer so much more annoying. The upside of this is that I've ended up learning how to install from source so I can avoid them when a deb package is not available!

I personally don't really like it, since it sidesteps what is supposed to be the all-in-one package manager for the system, and integration can be poor.

It's an alright idea, but I like the native package managers better. We're not Windows, we don't need so many different places to download our stuff.