First of all, there is no need for you to defend your qualifications. A sound argument should carry it's own weight, most people would agree. The fact that you spend all that time defending your own point of view really detracts from your argument.
Second, under the US law, Car Rental agencies are liable as owners of the vehicle regardless if the driver was doing something irresponsible. Thus, ISPs are not quite like Car Agencies, in that they not usually liable for infringements of its users. Additionally, allow me to add to the Judge's argument and hope that it makes some sense. Car Agencies rent out physical goods owned by the car rental itself, namely the vehicles. Therefore, the car agency will have liability as it was something owned by the agency that caused damage. Whereas, the ISP is a routing service. It does not own the data sent nor received. In that sense, it is more like USPS or any other mail/package delivery service. If someone mails some a DVD with copyright infringing materials on it, is USPS liable? Most likely not, whoever sent the package should be liable, along with the recipient of the package if they acquired the DVD to circumvent copyrights. Here USPS does not own anything that caused damage. Similarly, the ISP does not own anything that caused damage. The IP address certainly didn't do any damage to VPR. Hence ISP is not a potential defendant in the lawsuit where as the car agency would be. Hence it's not a very good analogy. VPR should have made the argument that you can subpoena the post office for where the mail was going to and where it was from. But then it's also against federal law to look at mail that wasn't intended for you, you wouldn't know about the copyright infringement.
Third, your vote-off terms are quite one sided. You have failed to summerize Judge Baker's argument correctly. It's not because you can sue the Car Rental in order to subpoena the identity of the driver, but rather, Car Rental agencies could be codefendants where as the ISP are not. This is a critical distinction in law since these two different firms have different legal protection in place. Not to mention if the ISP was a defendant, then the ISP would have to yield the identity of the customer during the adversial process. There would have been no need for a subpoena!
Fourth, you say that the Judge's writing is incoherent, what about this sentence you wrote? "If some customers in similar situations have had their identities made public by other circumstances, the judge's ruling gives no reason why that should be relevant at all, in a situation where the customer's identity is not public." I am going to ignore the fact that sentence is poorly constructed, but explain why the Judge's ruling actually supports his claim. He is using this sentence to support the fact that car agency analogy doesn't apply to the ISP. In the Car Rental case, there are also public records of the customer's information, and in the ISP's case there are not. Hence this is an additional fundamental difference between the two scenarios, so any analogy is not apt.
Fifth, about the whether or not IP subscribers are at fault, you claim that even if the defendant is not guilty, that could be proven in court. Unfortunately, that not how most of these cases work. Once VPR subpeonas the customer's information, they end settlement letters threatening very expensive law suits unless the "defendant" settles out of court (usually for several thousand dollars). Many users cannot fight this because they cannot afford a lawyer to do legal battles for a whole year. And at the end of the day, even if proven innocent, they could still be down even more money because they had to pay the lawyer. Unlike a criminal trial, this would be a civil suit and you do not have the right to a lawyer. Hence, a trail may not even happen, in which case you are punishing the wrong people.
That aside, you claim that the court must believe that there is a reasonable probablity that the plaintiffs will win; in reality is quite unlikely. It's highly possible (>90%) that the infrindger does not actually live in the jusrisdiction of the court, so the case would be thrown out before it goes to trial.
Sixth, you make the claim that IP are assigned to IP specific trackable users. First of all, you are more than likely to be behind a NAT at corporations and universities. Only a few of university have enough unique IP address for its users. So the IP address you have is most likely a router at the university or corporation. The next question is then can you still trace it to the user. Maybe. Sometimes it is still possible to see which packet is routed to which user, but ISPs and routers don't have to keep a running log of where each packet is from and going. Additionally, many universities have unsecured wi-fi networks on campus for its students and faulty to use. Sure you may have to sign on, but it's often easy enough to acquire a username and password by sniffing thanks to the fact that the network is often not encrypted.
As some of the users have already pointed out the linkage between IP Address and users is not actually unique in any direction. One IP Address can be shared by multiple users and one user can even have multiple IP Addresses. The important fact is that IP address does not link to users. I think you've watched to many CSI episodes where the police have super advanced tracing or facial scanning technologies. In reality, we are no where near that kind of sophistication. This is reality:
Gateway IP Address -> Router Mac Address -> NAT -> Computer Mac Address -> Computer -> User(s)
There is problem here though. MAC address are not necessarily unique. Not to mention there could be multiple users. Hence that Gateway IP that VPR has will most likely not be able to pin point anyone.
Seventh, you are correct in that the John Doe's only defense is to quash the subpeona. However, the quash doesn't actually protect the Doe defenant, because the adversarial process continues. As the adversarial process continues, even is the subpeona is quashed and as long as defendants are found guilty, the Doe who filed the motion for quash will be found guilty. Reason: motion to quash is public records, you have now identified yourself to the plaintiffs.
Eighth, You claim that the adding of 900 additional Doe defendants have nothing to do with the case, but it does. The issue is that if the plaintiffs get the first 100 users' information in a subpeona. Then when the plaintiffs add the 900 more defendants, the new defendants will have an opportunity to quash the subpeona. If the subpeona is quashed, the first 100 user's name should not be available to the plaintiffs either since it is the same lawsuit. However, the personal information has already been revealed to the plaintiffs. This is not acceptable.
Nineth, you are correct in that dismissing defendants is the right thing to do. But that's the judge's lead in to his next point. There are a lot of out of court settlements which is often used as a scare tactic. The Judge's job is to protect the people from abusive lawsuits like these.
Tenth, again you are correct that Judge Baker doesn't really point out why the the issue is more pronounced in a lawsuit against 1,000 John Does. But he should not need to spell it out for you. It's clear from the earlier sentence that significant number of John Does ends up coerced into a quick settlement.
Eleventh, the judge notes that the subpeona is clearly a "fishing expedition" in all intents and purpose. It is not healthy to promote such practices in court, as it opens the flood gates for companies to coerce people into settlements for no wrong doing.
Finally, the judge also points out that the court doesn't actually have juristiction over any of the John Does at this point in the legal process, since none of the defendants have been served. Sure this could be a shortcoming of our legal system, but at the same time, it protects us from large corporations from using the lawyers to be abusive towards the less legally equipped individuals.