Once "web" apps are using local storage and running offline and using the full power of the hardware, it's not clear what distinguishes them from "native" apps. Other than having to be written in the often-less-than-ideal HTML+JS+CSS, and even that isn't necessarily the case with NaCl.
I can think of at least one thing. When you are developing a web app, you don't have to worry about people using out-of-date versions of your app. On the flip side, when you use a web app, upgrades tend to be mandatory.
It's a completely different computing paradigm. The current model is "work offline unless you have some reason to be online" the cloud model is "work online unless you can't".
