The main point is the same one that PG brought up, that the transaction graph is very easy to follow and if the gatekeepers are compromised then most of transactions become transparent.
A novel point they make is that some group (probably the creators of Bitcoin) control 25% of the money supply. I have not read the paper yet so cannot comment but I was under the impression 95% of Satoshi's coins have never moved since being mined. (If he does control them at all) Of course if they do control 25% of all the circulated Bitcoins this would forever stunt its growth as that actor would always be far too powerful.
Whilst I do not believe a Government created Bitcoin I welcome these articles that counter my own views. This also re-emphasizes the work that needs to go into coinjoin or zerocoin implementations as soon as possible. Also we need to seriously fix the 7 tx/sec limit.