Flathub supports two repository types: Stable (master) and Beta.
Alternatives
Some applications (like Transmission) have QT and GTK interfaces. Currently, users can only access the GTK interface. There’s no way to use the QT UI unless someone creates it with a new APP ID. If we had an alternatives repository, we could put the QT version there without changing the APP ID.
Another example is PoEdit. It actually has two versions: PoEdit (Open Source) and PoEdit Pro, which is open-source-based but offers some extra paid features. If we had an alternatives repository, we could put PoEdit Pro in the alternatives repository without changing the APP ID.
We could also provide exceptions for alternatives. Currently, Flathub requires all submissions to be compiled from source code. If we had an alternatives repository, we could put AppImage/Snap/Deb derivatives in the alternatives repository without changing the APP ID.
Abandoned Software
Instead of marking games and other low-risk applications as EOL because they are dependent on the EOL runtime, we can move them to the abandoned software repository without forcing them to use a supported version.
Just brainstorming.