Even examples of "web with native wrapper" apps, like Facebook and OkCupid, are dramatically, dramatically worse than best of breed native apps.
Companies like OkCupid and LinkedIn, whose apps both rely heavily on web views, need to think about the benefits of using the same code across multiple platforms. I'd tend to argue that both of those apps are pretty well-done. They certainly lack some of the really slick transitions and polish of an app like Tweetbot, but I definitely don't think either one feels cheap.
If we're to believe that one day HTML5-based mobile web apps will rule, what is wrong with PhoneGap exactly?
To me, it's like using Java for a Windows desktop app.
Do you just have a problem with the native components that are all always there versus just the shim pieces you need, etc? Any evidence that that really causes any sort of perceivable issue? It seems like it would all be microscopic compared to... anything else in a real application.