Indicators (which are menus created though a DBus interface) simply have no place in the gnome-shell, so the library was not merged into Gtk3 (the reasoning was that only things common to all consumers belong there). Transmission uses indicators when available but falls back to using status icons when not available. This makes it a second-class citizen in gnome-shell, even though it works.
I think the issue was actually making transmission behave better under GNOME. The discussion in the bug report even provides a patch that doesn't alter the behavior of Transmission when running under other platforms.
And it's happening to users, who are being told their concerns about GNOME3 are irrelevant, and also to developers, who are being told that "you have to decide if you are a GNOME app, an Ubuntu app, or an XFCE app." (direct quote, btw.)