Okay, so after alot of searching and trying i found a solution to show the hidden application menus in my system.
Please Note: The original gnome-shell, without being tweaked, does not have this issue.
The issue mainly is caused by GlobalMenu which appears to be Not Supported under the Gnome3-fallback mode just yet.
So what I did was Disabling the GlobalMenu and got my Application menus back once again, and here's how i did it:
First, we need dconf-editor so we're going to install dconf-tools
sudo apt-get install dconf-tools
after installing, Press ALT+F2 and Type dconf-editor and press Enter.
now navigate to org/globalmenu and uncheck enabled.
You may either log out and log back in or restart your system and the Application menus will be ready to be used once again.