Using the native function calls directly save all the memory/cpu overhead. It is extremely important in a resource constrained device.
Looking at the "iPx" devices as they have been thus far, since each app gets complete use of the device at a time, this is really a non-issue (except for excessive CPU use which can diminish battery life). If an app has free reign of the device and nothing else can run at the same time, who cares if it eats a bit more memory? It's not like it is taking it from somewhere else where it could be used. And if it is too much for the device to handle, Apple already has a policy of rejecting such apps.
Now, of course, with their announced "multi-tasking", they're probably going to claim it has become an issue. But let's get real here. The "multi-tasking" of which Apple speaks isn't real multi-tasking as we understand it on a desktop environment. Except for things like background network traffic ala Flickr uploads, etc, for most apps, this is just fancy task switching. The app is even completely unloaded from memory (so much for the "memory hog" argument). The only time it isn't is if it uses one of the 7 supported background processes, which I'm sure will still allow the bulk of the app to be unloaded from memory while it is in the "background". Apps that use these background processes and don't play nice can be rejected (there will be such apps regardless of the language used).
So I'll say it again, in the end, this doesn't really improve the user experience for these devices. If anything, it ensures that all those less-skilled developers out there are going to be forced out of their safe sandbox where they're less likely to do harm and into using tools that are much less forgiving and much more error-prone in the wrong hands. I think Apple is going about getting what they want all the wrong way. All they need to do is raise their app screening standards to screen for interface consistency, memory use, and general platform guideline compliance. It's just plain silly to restrict the language used.
And on another angle, consider some of the 3D games out there. Do they honestly expect each developer to write their own full-on iPhone-specific 3D game engine? The best examples in the App store at the moment are either using a 3rd party engine of the sort that this new policy would ban (i.e. Unity 3D), or belong to a well-funded major publisher like EA who can invest developing their own quality engine. So basically Apple must not realize that this policy is going to relegate the rest to producing lots of bad-looking, buggy shovelware. Way to go, Apple!
High-level frameworks can be your friend. When they're not put to good use, just screen those apps out. Don't throw the baby out with the bathwater.
