There's been a big debate in the media over whether HTML5 or native apps will win on the tablet. The answer is clear to me: Native apps will. Why? Because they can do more, and they can better take advantage of the touch and other native capabilities of the iPad.
In my everyday work, I find that I use mainly native apps on my iPad, even when a website is available (such as Twitter, YouTube, various news sites, Dropbox and Box.net, and several of my banking services). The Web "apps" I use tend to be cloud services that both run decently in the iPad's browser and have no equally capable app available. The Concur travel management system is an example, as is Adobe's SiteCatalyst Web analytics tool and U.S. Bank's banking site.
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As someone who uses a tablet several hours a day, as well as a smartphone and computer, I can tell you from experience that apps based on HTML and AJAX have real deficits due to their technology that limit when they can be used successfully on mobile devices.
For example, interface elements often assume the use of a mouse, so they aren't good at handling the gross motion and size of fingers versus mouse pointers. There are no equivalents for several scroll and selection gestures, so some standard HTML and AJAX interface elements -- such as drag handles -- don't work on an iPad or iPhone, Galaxy Tab or Droid.
Content blocks often don't fit well to the screen, and their nonadjusting margins make the text effectively too small to read easily (if you zoom in, you have to pan back and forth for each line). Gestures are also not supported, so navigating through rich HTML websites can be impossible.
Flash is no solution, either. On the two mobile platforms for which it is available (Android and the defunct WebOS), it has the same UI issues as HTML and AJAX, plus performance and functional incompatibilities that essentially restrict its use to watching videos and animations.