The global filesystem is only a problem if you run lots of closed source/untrustworthy apps. Many of us don't and use the global filesystem very heavily and very much hope it does not go away.
An average user is a myth. Every kind of average user has its own traits and they differ widely.
That's why there is such thing as system settings.
And yes, most desktop users are conscious when they work with files. Windows by default suggests "My Documents" folder as a target destination which is a pretty sane safe choice for all traits of average Joes.
Honestly I think not having a global filesystem makes things harder for the "average user." Most college students aren't going to only keep their word documents in word for example, they need to email them and upload them to tools like blackboard.
I guess you also only then need a firewall, if you use closed source software. When using OpenSource software you can always be sure that nothing will do unauthorized access to your network, willingly or accidentally...
Every time I call my mum I have to call my dads mobile first because she can't remember to press the button to hang up. Ther's only so much simplyfying you can do.
Funilly enough, in her 70's now she's taught herself to use a computer and can manage documents in the file system.