The traceable public block chain is a big improvement over cash in their ability to associate and track.
The proportion of the block chain that can be associated with identities is likely to be a super majority. Research has supported this and that research didn't have the data about every IP address association that the NSA does. And the fact that your IP address is almost never obscured (and the governments can remove your anonymous WiFi Hotspot and unregistered, prepaid mobile device options) strongly supports this conclusion.
If you are referring to the paper "An Analysis of Anonymity in the Bitcoin System " by Fergal Reid & Martin Harrigan, please note this very key statement in that paper:
Much of this analysis is circumstantial. We cannot say for certain whether or not these flows imply a shared agency in both incidents. However, it does
illustrate the power of our tool when tracing the flow of Bitcoins and generating hypotheses.
Your magic NSA database of bitcoin-address-to-identities would be a large collection of circumstantial evidence, not definitive proof of associations to identities. It could be used as probable cause for search warrants and subpenas, but without collaborating evidence, it is worthless by itself in an actual domestic criminal case.
Likewise, a magic NSA database of ip-address-to-identities is also circumstantial. I may pay the bill for my residential internet service, but I allow my friends to use my wi-fi, the logs that associate their device's mac address to activity on my LAN is overwritten within 7 days. I may be circumstantially suspect of any crimes committed through my residential IP address, but it is not definite proof.
If I were hypothetically motivated to commit some financial crime, I would most likely walk a kilometer to the large state university in my town, connect to the guest wi-fi network covering the entire campus and do my thing. All they have is the mac address of my tablet and maybe some geo data. If that tablet is never discovered by warrant, never registered or otherwise associated with me, it can't be used as evidence linking me to the activity.
You make the claim that "governments can remove your anonymous WiFi Hotspot." I would like to see a reference to a paper explaining how this is done, or an understandable explanation based on facts.
Unless the standards of evidence drastically change in the USA, I don't see how the government is going to prosecute and march off 10,000 financial criminals to ass-rape prison. The idea is ludicrous, since there are plenty of financial crimes NOT involving bitcoin committed on Wall Street every day, and I have yet to see an assembly line of prosecutions.