If you use UIWebView, where you download your WebApp, you use a version of WebKit that does not support JIT optimizations for JS ( source )
I will break the application in smaller parts and try to show something to the user as soon as possible, and then continue loading JS in the background. I know this is bad, but if your problem is a heavy JS application, you are stuck with the UnIT JIT WebKit engine (AKA UIWebView).
Take a look at WWDC 2012 Session 601: Optimizing Web Content on UIWebViews and iOS Web Sites (You Must Be a Registered iOS Developer) and hear this episode of Cocoanetics Podcast
I would like to know some optimizations, however.
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