It's true, there are a handful of iPhone applications that are actually better than the original apps they replace — Facebook, for sure, and my recent fave, the Zipcar app among them. Of course the original ones — the "Desktop ones" referred to in the article — are actually web applications.
The fact is that, despite the push towards — and what many believe is the inevitability of — the web as the primary source of applications, native apps are still vastly superior in almost every instance. This is why Apple had to finally give developers — and consumers, of course — the App Store. Web apps just weren't cutting it on the iPhone. And while they do somewhat better inside a full-sized browser on a full-powered computer, I still think web apps have a long way to go — a very long way — before they'll ever rival the experience of native apps. Platforms like the iPhone and continued interest in things like Site Specific Browsers offer very convincing evidence that native apps will continue to thrive for a long time to come. To be honest, I have my doubts that web apps will ever completely replace native ones.
I should also point out the probably obvious fact that there are certain apps that will always be best on a mobile platform because they just happen to be particularly well-suited to mobility. The Zipcar iPhone app is a perfect example. It's an app for finding, renting and controlling cars, for Chrissake. Where better to have an app about travel than on a mobile device? In fact, having the Zipcar app on an iPhone gives it certain powers the web app will likely never be able to match. But I'd venture to say that there are very few, if any, application experiences that are better in a web browser than they would be in a dedicated, native app.
No doubt about it, web apps are supremely useful, especially for certain tasks. But that's like saying the web is useful. The ironic fact that many of us prefer surfing Facebook on our iPhones to using the original web app version on a full-sized computer should give you an idea of just how hard it will be and how long it will take to supplant native apps with web apps.