I would say that the main points are performance, access to hardware apis, and - the most ignored one - ease of install.
There is no familiar way for users to install a web app (unless they are a bit tech savvy). My uncle adds favorites to its home screen to go to web pages, he knows that, and its impossible for him to think that a website is a website and if you add it to the home screen "turns out" to be like an application.
If a clearer interface was provided in the mobile phones, something like identifying webapps with a meta tag, or something, so that the phone could know and offer the user to install the app, the barrier for mobile webapps adoption could be lowered a lot.