Agreed on all points, really, though less so on intuition.
Regarding A handheld device is not a small desktop device, which overlaps Screen real estate matters anyway, I think the Hildon idea of no overlapping windows is really a good one. And I think full-screen apps should be default. But that said, I think the ability to have some non-app stuff on-screen is really good. I feel that a lot of space is wasted on the N800 in non-full-screen mode. It should take off just the left side, or just the top, but not all 4 sides, as it does now.
Let me add:
Orientation should work
If desktops can do it, why can't my N800, where it's so much easier to rotate between portrait and landscape? Yet it's left to apps to support, so very few do support it. And, in the N900, a sensor for it would sure be nice.
We need multi-touch
Not sure what to do with multi-touch per se, aside from finger-painting software. But it enables resting your hand on the screen and still using a stylus, enabling you to write on the left half of the screen.

But we should also learn from the iStuff disadvantages:
Hardware buttons are good
But they could stand to be a lot better than their current state.