I think D-bus has many problems and isn't very good. I also think the sandboxing (of Flatpak and other systems) has problems, e.g. lack of some kinds of permissions (e.g. permissions that depend on command-line switches, permissions to execute user-specified external programs by popen (without the restrictions affecting them too), and more), inability to properly use character encodings, etc. There are other issues as well, even though I think that the sandboxed execution is not a bad idea in general.