So I think what you're alluding to is that although Gnome Shell presents a version of the "Applications" menu, it doesn't (AFAIK) present the "System" menu anywhere.
So, you have to still might want to add a launcher for the tool you want to run somewhere in the Applications menu tree. That's easy but not trivial:
- click on your name up in the upper right hand corner
- click on "System Preferences..."
- click on "Main Menu" in the Look-and-Feel section of the "Control Center" that pops up
- select the section where you want to add the software-center launcher - I chose "system tools"
- click the "new item" button
- enter "software-center" as both the name and the command
- click "ok"
- click "close"
Now when you select "Activities" in the upper left hand corner, then the "more" button just to the right of the word "Applications", you'll see your new software-center launcher listed in the system tools menu.
I tried this and it worked perfectly.
-pbr
EDIT: I don't know why I didn't see it there; it appears there's already a launcher for this; "Ubuntu Software Center" is a launcher in the "System" section of "System Preferences..." control center.
I haven't verified, but it looks to me like GnomeShell is presenting the Applications menu under that "more" button I mentioned above, and presenting the System menu within the control center that pops up when you choose "System Preferences..."
