I'm in agreement with the article. Most of the desktop-mimic web apps I've used just plain suck. They feel like really slow, crappy desktop apps, as if you were running Lotus Notes on a 10-year-old windows machine, only worse.
This isn't to say that 'web'-style interfaces don't have room for improvement, but it's a different ballgame than the desktop. On the web we have load time concerns, a different toolset for building the interface, and different considerations in terms of color and space.
Not to mention the precedents set by every other web page that has come before which people are used to. Geez, we have to do a scriptaculous hilite on every xhr just so people will notice what's going on.