The main tangible difference is that we enable you to push out incremental updates to your app, immediately. And to do so in a way that your app feels completely native. PhoneGap does not offer this. The only way to do it with PhoneGap is to actually point their UIWebView instance at a URL on the live internet, which makes your app slow. That, or you'll have to build a lot of complicated syncing and caching and updating stuff, which is what we've built.
The second difference is more philosophical. That is, for most apps, we don't believe that you should attempt to write a whole app inside a web view. It just leads to apps that don't feel native. So our approach, and the one that Clutch has been tuned for, is where you build most of your app using native tools. Then, you use Clutch to build out certain display areas using web tech.
I hope that answers your question.
Like I mentioned in another thread, similar "push updates" mechanism have already been banned by Apple. (I don't know, why am I downvoted for informing HN users).