The point of a nexus device to me isn't ONLY that it runs a stock version of Android. That much I agree is arguable and completely up to preference. Some prefer the other skins and some prefer the simplicity of stock. To me it's the updates. When google makes tons of great additions to the OS which they'll inevitably do when they jump to 5.0, it will suck balls to wait 6+ months to get it on your device.
To me if OEM's can get updates REALLY fast then yes nexus devices are no longer needed and they are overhyped for sure. But until then, meh. And of course google needs to do a lot better with their OS. They're lacking a bit in features that are available in other skins, but they'll get to it.