I don't think the EFF is going to win this one. It's not because of some government conspiracy, or the odds being stacked against them or anything like that, but rather because their argument is flawed. As detailed elsewhere on the EFF's site[1], the core of their case centers around NSA's Section 702 Upstream collection. They have more recently hinged their argument on the Privacy and Civil Liberty Oversight Board report on Section 702[2], but the case predates it going back as far as Mark Klein's Room 641A disclosure. The identifiers that the EFF talks about are described in the report as follows:

As noted above, however, all upstream collection — of which “about” collection is a
subset — is “selector-based, i.e., based on . . . things like phone numbers or emails.” Just
as in PRISM collection, a selector used as a basis for upstream collection “is not a ‘keyword’
or particular term (e.g., ‘nuclear’ or ‘bomb’) but must be a specific communications
identifier (e.g., email address).” In other words, the government’s collection devices are
not searching for references to particular topics or ideas, but only for references to specific
communications selectors used by people who have been targeted under Section 702.

In other words, the NSA is searching for the communications of specific people - it's targeted collection. The EFF itself even concedes that they are filtering out wholly domestic communications[3]. Instead of questioning the specific procedures for targeting these people, the likelihood that they may fail and collect an innocent bystander's communications, the procedures dealing with incidental or accidental collection, etc., they are instead taking the stance that the filtering itself is illegal because a packet filter needs to see a packet before determining whether or not it matches the specific communication. As an analogy, if where to pull up my terminal and run:

$ seq 1 3 | grep -v 2 | grep 3 > out.txt

... the government is arguing that the collection is the contents of out.txt ("3") and furthermore, they put an extra measure in place to ensure that the number 2 (i.e. purely domestic communications) is never collected. The EFF is arguing that 1, 2 and 3 are all collected because each one exists in grep's buffer for a millisecond before it is discarded - it doesn't matter that it's never seen by a human, entered into a database, written to disk or transmitted elsewhere.

I think I see why the EFF is making that argument: in Clapper v. Amnesty International it was ruled that the plaintiff didn't have standing because they couldn't show that their specific communications had been collected. Jewel v. NSA would likely have the same issue, so to get around it the EFF is instead arguing that the very fact that the NSA is conducting any sort of packet filtering itself constitutes a search and seizure, regardless what safeguards are put in place or whether the filtering is targeted. I think they're grasping for straws with this one - I'd be really surprised if they win. If I were in their place, I'd probably FOIA the hell out of the 702 procedures and look for loopholes instead.

[1] https://www.eff.org/press/releases/eff-asks-judge-rule-nsa-i...

[2] http://www.pclob.gov/Library/702-Report-2.pdf

[3] https://www.eff.org/files/2014/07/24/backbone-3c-color.jpg