I definitely agree with you that from the historical perspective that Cocoa is the "Native" API. And after experiencing it (and having been a long time developer on the Java platform), I think that I would have really liked a Mac OS X without Carbon. But now that Carbon and Cocoa have been mixed, shaken and stirred into OS X, the historical perspective does not serve us that well. Just like the historical perspective of Java having been originally developed for small machines like interactive TV boxes doesn't do service to the current reality of Java in the enterprise.
With that in mind, I'm pretty happy to see the two sets of APIs co-exist, share functionality under the cover, and even build on each other. And after seeing Scott Forstall talk about how they go together, I have good hope that they will be able to develop both without undue harm to either.