I can list a ton of APIs that are available to native iPhone apps that aren't available to apps via Safari. Push notifications being the most notable, in part because they are purposely not supporting an open standard.
> Me neither! That's why we need 3rd party app stores.
Nope, not at all. You want 3rd party app stores because:
1) you don't believe Apple's walled garden is worth a 30% cut
2) you dislike Apple's lack of transparency in their app review procedures
3) you're unable to sideload an app onto your "customer's" devices
One or more of those are why you "need" third party app stores. And, I think you've got a valid argument for any of them. But none of those have anything to do with what APIs are available to websites in Safari.