WebSocket, Canvas, Web Workers, HTML5 drag and drop API, WebGL, O3D, Application Cache API, Chrome/FF (and possibly other browsers) allow web apps to open mailto: links, FireBug, Web Developer Toolbar, etc. etc.
Unless you actually refute EVERY SINGLE OBJECTION, apps still win, at least in the user-experience sense. Something as small as not getting an hourglass when the app is "thinking" is a bug, which every web app has right now.
Well, that's pretty subjective. I prefer GMail's user-experience than any competitive desktop app, same for Google Calendar, Google Reader, Basecamp and FreshBooks. I guess I'm biased as I am a firm believer that the open web is the platform of the future. That being said, I totally agree that there is still a lot of room for improvement, but we're on the right track :)
It's pretty trivial to turn the cursor into an hourglass with CSS. That isn't a limitation of web applications.
Then why do nearly none of them do it? Probably because they can't judge when they will stutter and lag - so many layers of web indirection.
The fact is, most web apps only a mother could love. The rest of us are sitting stunned and silent when someone shows off their latest "jewel" which stutters, lags, has buttons that don't react when pressed, takes 3-5 seconds to put up/take down a dialog based on a server database query...
I don't know what most of those things are, and I'm guessing most of the world doesn't either.
Most people don't know what HTML is, yet they can use web browsers. Not knowing HTML 5 will not prevent them from using HTML 5 -- and HTML 5 is covered by the first half of that list. The mailto extensions don't have to be -- they could as easily be built into the browser (and should be by now). Web applications can already be online/offline hybrids (Google Gears already provides the functionality, HTML 5 adds it as well).