app store doesnt do SOFTWARE and CRITICAL updates

This is now happening on 3 computers. Started in Lion. Had it in Mavericks, Yosemite and still in El Capitan.

Can't really blame this on the OS.

I've updated to The App store wont do the software updates but the third party apps do!

How can I update Safari and Raw Camera and Pro stuff if they don't come in a standalone?

And yes..I was on with a apple support specialist from CA and we spent a few days going over reinstalling OS. (which I just did again)

Signing out..signing in

Checking if port numbers are open.

Ran some terminal commands.

..etcetera etcetera......blah blah..you name....it we did it.

I will NOT erase a drive and reinstall and spend a day or two getting thing back to what it was.

APPLE FIX YOUR APP STORE SOFTWARE UPDATER!!!