The coursework would be very focused on understanding the internals of each layer of the stack. To make a comparison to the auto industry: Your training won't result in you being a mechanic that can follow the manufacturer's manual: you will be the person that can write the manual because that's how much you understand how the car works.
But the real change I'd like to see is how the labs are done.
When you enter the school they give you 12 virtual machines on their VMware cluster (or Ganeti cluster).
In phase one you go through a progression that ends with turning those 6 machines into 2 load balancers, 3 web servers, a replicated database, a monitoring host, etc. (this is done as a series of labs that start with setting up one web server, then building up to this final configuration).
At that point the CS department turns on a traffic generator and your system now gets a steady stream of traffic. There is a leader-board showing show has the best uptime.
Phase 2 you set up a dev and qa clone of what you did in Phase 1, but you do it with Puppet or cfengine. Eventually those tools have to manage your live system too, and you have to make that change while the system is in use.
Once you have a dev->qa->live system and your uptime stats become 20% of your grade.
Another element I'd like to have is that there is a certain point in which everyone has to run other people's system using only the operational documentation that the creator left behind.
There might be another point in which the best student's cluster is cloned to create a web hosting system that provides real service to the community. Students would run it cooperatively, maintaining everything from the software to the operational docs.
However, by the time you get your degree you'd not only know the technical side of system administration but you'd also have the practical experience that would make you extremely valuable in the market.
Update: To be clear, there should be gobs and gobs of theory. I would want the above to be the labs that match the theory. For example, theory on OS matched with Linux kernel as an example; theory of autonomic computing with cfengine/puppet as an example, and so on and so on.