I think it was very wise to dismiss the naturalization claims and the Fraga case as precedent to be used here. What lies before you is obviously proving the commonality of these cases and that there are bureaucratic inefficiencies that are slowing this process down. The one way to do that, as the judge almost suggested, is to get more people to join the plaintiff list and to ensure their cases have different backgrounds, classifications, etc. I also think that the plaintiff list should include as many as possible long suffering folks, perhaps 2001s and early 2002s. It will be however, exceedingly difficult to argue a class action, because they can prove that various subclassification drastically affect processing time. So, having long standing EB1s, EB2s might be a good argument against that.
I also think that USCIS will not have a problem in proving a lack of resources and sort of a compounding effect on the backlog. The thing to point out here would be the "reshuffling" of that queue, which can have absolutely no security application. In other words, prove that FIFO is not being utilized, perhaps in order to quash some of the applicant discontent by approving the new applications faster, therefore isolating a single group of applicants (2001-2002). By proving that the new applications are being approved in a "reasonable amounts of time", they can argue your class action point down as well. I think that it is reasonable to assume at this point that you will not be granted a class action.
The discovery process will also be a tough one because, again, per the judge, the government does not like these kinds of things. The process that is used is not public knowledge and for matters of national security, they might argue, cannot be divulged in its entirety. What the discover process should serve to do is, factually, prove that, due to lack of organization and proper priority, files are being processed out of order.
So, in summation, I don't know if the case is that strong. You might have a point that SOME cases take a long time, but they will argue that not ALL the cases are delayed.