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.