I’m a big fan of Fedora Atomic. However, even I have to admit that knowing how to install packages through dnf is simply more convenient than knowing and understanding the nuances between rpm-ostree, Toolbx/Distrobox and flatpak. And I haven’t even delved into ujust and brew that are found on uBlue images.

Furthermore, even if we would limit ourselves with what Fedora Atomic prescribes, we see the following inconveniences:

• rpm-ostree ; I know --apply-live exists and I know systemctl soft-reboot exists. But still, if you have to resort to rpm-ostree, then both the speed of update/installation as well as the need to reboot (or live on the edge with --apply-live) are inconvenient compared to dnf.
• flatpak ; It’s inconvenient that I have to alias the installed package if I prefer sane naming conventions when accessing it through the terminal. Furthermore, stuff like the NativeMessaging portal not being available yet for sandboxed browsers and how that prevents any local password manager to interact with them (without hacking your way through; which, once again, is an inconvenience) is inconvenient.
• Toolbx/Distrobox ; the fact that you’d have to setup quadlets (or simply rely on uBlue images to do it for you) to keep them up to date, up and running is an inconvenience. The fact that distrobox-export has to be resorted to for accessing these directly from your ‘App Drawer’ is an inconvenience.

The fact that there’s no centralized place for upgrading all of the above (unless you rely on an uBlue image) is an inconvenience.

I could go on and on, but these should satisfy in revealing some of the more obnoxious inconveniences.