According to https://bugzilla.redhat.com/show_bug.cgi?id=1274451 not allowing graphical user interfaces to run as root is a design decision of wayland. The way to go for synaptic would be to run the graphical user interface as the unprivileged user who has called the program and then to use polkit in order to gain root rights for the portion of the program that does the actual installation and uninstallation of packages.
** Bug watch added: Red Hat Bugzilla #1274451 https://bugzilla.redhat.com/show_bug.cgi?id=1274451 -- You received this bug notification because you are a member of Ubuntu Bugs, which is subscribed to Ubuntu. https://bugs.launchpad.net/bugs/1551951 Title: synaptic does not run over gnome wayland session To manage notifications about this bug go to: https://bugs.launchpad.net/ubuntu/+source/synaptic/+bug/1551951/+subscriptions -- ubuntu-bugs mailing list ubuntu-bugs@lists.ubuntu.com https://lists.ubuntu.com/mailman/listinfo/ubuntu-bugs