To help me structure the courses I teach better, which turns out to address some of your issues, I built the Morea Framework:

http://morea-framework.github.io/

Here's the Morea-based site for the software engineering class I'm teaching starting on Monday:

http://philipmjohnson.github.io/ics613s15/

One could imagine a wrapper around a set of courses structured using Morea that would get close to what you desire.

Philip