What web apps need desperately in order to become true first class citizens is support for keyboard shortcuts across the board.

Doing Alt + <Key> should bring up the appropriate menu in the web app not the web browser.

Doing Ctrl + S should ask the web app to do a save , not ask the browser to save the .html page.

Of course this is all stuff that could be abused by aggressive websites so there needs to be a distinction between apps and pages.