User perceptions play into performance more than you'd think. If the HTML app can't scroll or transition smoothly, or it's spinning up new WebViews and you have to wait (there is an inherent delay in loading any content in a new UIWebView), then users will say it's slow. Not to mention memory usage of HTML elements, and managing that whole mess (the "rococo pandemonium" of HTML CSS and JavaScript, as Tim Bray put it) of objects in (usually) one giant container...
I've never found a situation where a WebView-based app is better than native.