The new medium has been born, but the old one is still being abused, so the split isn't complete and won't be until this no longer happens: http://xkcd.com/1174/
The worst is LinkedIn, which will send you an e-mail with article links it it, and if you click the links it takes you to your browser, which does the thing that xkcd comic describes if you don't have the app installed, but if you do have the app it just launches the app and leaves you at the home screen, and the context of the link you clicked on is gone.
I'm wondering about the "can't zoom" bit. I can't zoom on many websites - because Mobile Safari has sold out control to the web developers, instead of acting as my user agent.