can sometimess not even respect your gtk/qt theming
sandboxing/permission system can lead to you trying to figure out which directory you need to give access to when you want to save file if it wasn’t preconfigured
uses its own libraries and not system libraries, want to play the hit new AAA game with steam flatpak? get fucked it requires a mesa commit that was merged 8 hours a go and you’re stuck on 23.0.4 and can’t use the git release.
Flatpak probably has it’s specific uses like trying to use one piece of proprietary software that you don’t trust and don’t want to give it too much access to your system, or most GUI software clients having an easy way to install Discord on your Steam Deck (no terminal usage, Linux is easy yay), but native packages 99% of the time work better.