Wayland is still customizable, and x11 isn't going away. If you want to trade in security and maintenance for features and capabilities, nobody will try to stop you. In that sense, distributions still don't hold much power over the user besides what they present as default.

> The fact that the same organization hosts flatpack but has not vision of how to use the capability model for Wayland really poses questions on the vision.

I disagree, and I'm a staunch GNOME skeptic myself. Flatpak and Wayland were both built as extensible systems from the start, and GNOME's implementation of both technologies is just one interpretation of the protocol. KDE is a good mirror example; their Wayland implementation exposes many features completely unavailable on x11, and their Flatpak permissions are integrated right in the Settings app.

Personally I don't like GNOME's approach to the desktop anymore, and I refuse to defend most of their more opinionated decisions. Those choices have a minimal impact on desktop Linux outside of GNOME though, and it more feels like Red Hat is displacing the amount of work put into keeping legacy systems alive.