Keep the shell format
For the chrome browser, i liked how when the notification or icon was clicked, it opened up either a new mini window or a self contained screen on the browser. The new full window gets annoying.
If you could find a way to emulate the fuctionality of the google+ extension for chrome, such that it shows how many unread on the actual icon, and when clicked, opens a shell window with the text thread updates (much like your actual screen on an android phone), and then you just click on one to reply.
Then with the notification popups, they continue your mini window reply.