Performance is generally much slower. This isn't a problem for most apps, but it is for CPU-intensive apps. That includes anything with substantial rendering or computation. The latest HTML5 features like local storage, sockets, and cross-window messaging go a long way to make many more apps feasible, those features aren't available in all browsers.

Even writing native Cocoa apps on the iPhone requires lots of optimization in loading and rendering content. JavaScript is even more intensive, making it more difficult to create fluid interfaces that rival the native experience.

I suspect that if mobile performance was comparable to desktop performance, Javascript would win out for a lot more use cases than it does right now.