Is the 2016 implementation of Shor's algorithm really scalable?
The main thrust of Cao and Luo's argument is that in the variant of the algorithm that was implemented, the first register—that eventually contains the output—contains only 1 bit. And if you only get 1 bit of output from the algorithm, that's insufficient for factorization. (For one thing, although this isn't their argument, 1 bit clearly does not contain enough information to determine the factors.)

What Cao and Luo seem not to realize is that for the variation of the Fourier transform with only one bit in the first register, the same value of $c$ is output as in the standard factoring algorithm; it's just output one bit at a time.
This change doesn't affect the $O(\log^3 N)$ running time. 

To try to be fair to Cao and Luo, they say that they don't think this algorithm works, and if it does work, then it isn't Shor's algorithm because it doesn't exactly match the algorithm described in the original factoring paper. A quote from their paper: 


  Finally, we would like to stress that if the implementation is indeed credible then it would be a new quantum factoring algorithm, not the Shor algorithm, because all requirements of the original Shor’s algorithm are not satisfied.


And indeed, it's not the algorithm from my original factoring paper. It uses the phase estimation procedure from Kitaev's factoring algorithm, and a variant on that, discovered by Griffiths and Niu (not by Parker and Plenio, as I said in a previous edit of this answer) that lets the algorithm output the estimate of the phase one bit at a time.