* Native performance.(getting better, still not there).
* Offline is way harder (possible, with manifests, but harder).
* Monetization is harder: you can't just 'sell' a webapp.
* The appstores (can be) a great distribution and promotion channel.
* The web has way less access to the device: No contacts, camera, etc.
It's getting better, but native apps do have their advantages.
What's wrong with the following pattern: 1. build an HTML5 app 2. build a native app that embeds a Web control 3. package the app and HTML5 app together using application cache 4. distribute on AppStore
You get the a) offline support b) monetization c) distribution via AppStore
Also, multi-touch is actually supported by webkit. There a nice WWDC video that intoduces this capability if you'd like to learn more.
To be clear the idea above isn't new of course. For instance http://www.appcelerator.com/ provides a native app with a thin wrapper around a web control.