-Weak processor.
-Non-1080p screen.
-Too thick (If it doesn't have Maxx battery life).
-No multi-window (Ala Samsung) feature or indication that stock Android will implement this soon.
Software optimization only applies to its weak processor, but software optimization is greatly overrated, and demonstrably so. Having used multiple generations of Nexus devices and skinned devices, I can conclude that while there may be some slight performance edge (Much slighter than people wish to admit) in favor of stock devices in comparison to skinned devices of the same generation, the truly determining factor of performance is hardware. For example, the performance difference between the Galaxy Nexus and the Nexus 4 is greater than the performance difference between the Nexus 4 and the Droid DNA. The Nexus 4 is faster than the Droid DNA which is faster than the Galaxy Nexus, and the DNA has a 1080p screen at that.
So if this claim people wish to make is true, that the Moto X, which is perhaps two processor generations behind the curb, can through software optimization alone supersede the speed of a skinned top tier phone, then without question the Galaxy Nexus should be faster than the Droid DNA, given that the Galaxy Nexus is closer in generation to the Droid DNA than the Moto X will be to something such as the Galaxy S4, and given that the Galaxy Nexus is a more truly stock device than the Moto X. But alas, this is not the case to be found, and we may thus conclude through rational study of the empirical data that the Moto X will be slower than the giants its proponents wish to sent it to battle against.
Also, the Nexus One didn't even make it to 4.0 and it came out with bleeding edge specs (Another testament to the power of specs against optimization), so good luck with your updates.
And I wonder how they'd even be able to hit a mid-range price point by building it in the US, if not from Google subsidizing it. It would be quite a laugh to see people defending it if it ends up being $600.