Such a long post probably deserves a long reply, but unfortunately this will be neither long nor thorough. I think you're right that desktop apps and web apps are conceptually the same, in terms of complexity. The difference is they are not the same in terms of "physical space." The interface is, by necessity, much different. Dealing with people where I work, it seems interface issues make up a large amount of the problems with traditional desktop apps. By comparison, web interfaces are very simple, and usually fairly similar: fill out a form, click submit; click a few links here and there. There's just not as much there to be confused by. Of course, I'm sure a determined developer could confuse the bejesus out of their users with any interface, whether web-based, desktop-based, or even paper-based, but that's a whole different topic.
