> a concept of an "app" makes no sense on a modern desktop, and windows is what users want to manage, not "apps"

I disagree; I think this is a subjective thing based on one's usage habits. I tend to think in terms of apps, with multiple windows attached to each. (This is partly because I keep a lot of windows open, and tabbing between 5-10 apps is more reasonable than tabbing through 30-50 windows.)

I agree with your main point, however; Ubuntu should be blazing its own trail, not mimicking the past.