I hate to say it but I would never use an iphone web app over a native one. It's less about looks than it is about feel / responsiveness. You also will always be stuck dealing with the forward button / back button structure.
<meta name="apple-mobile-web-app-capable" content="yes">http://nrbd.tumblr.com/post/55066018/apple-mobile-web-app-ca...
http://lists.apple.com/archives/safari-iphone-web-dev/2008/O...
Furthermore, web apps can be created that explicitly manage data and assets in a local store. Web apps can be quite responsive if they take advantage of this.
A native app will likely be more responsive, but a web app isn't as limited as you seem to think.