What do you call MobileMusicPlayer.app? MobileSafari.app? YouTube.app? Are those not native apps? I mean, SJ touts the iPhone as being the most advanced mobile platform on the market, running a mobile version of OS X - what does that imply? A modified version of a desktop OS: of course you can install native apps. I mean, that kind of goes without saying. Then the iPod Touch is released, essentially an iPhone minus the phone (and initially crippled by not including apps already developed for the iPhone, a situation Apple was quick to remedy - for a fee) ... Same deal. A modified OS X with a handful of pre-installed apps.
So, obviously the iPhone/iPod was meant to handle native apps, it comes loaded with them! Just because Apple didn't advertise it as being expandable doesn't mean it hasn't been since almost the beginning.
Some people don't need Apple's marketing team to tell us how we can and cannot use the products we purchase. Think different.