Would have been a lot more clear to say "the redacted bits are from patents approved by the USPTO." I hate having to go on easter egg hunts to confirm if this is something I should care about.
And for Cassini2 specifically, it's not an issued patent vs. rejected patent. Both were issued, the point being that the new one was issued after the first was invalidated by a district court. And about 5 months after Alice. And the second was a continuation of the first, not a new patent. That's why they are so similar, and probably why they didn't halt the process and re-evaluate it.
USPTO wanted comments on the guidance, not pointing out where they are failing to meet the guidance. This is where the EFF probably overstepped.
I have a problem with this part. The Alice decision was basically "adding a computer doesn't automatically make it novel" - the court did not agree that "adding a computer automatically doesn't make it novel" - those are two distinct ideas. And what the EFF pointed out in the chart was that two allowed patents were basically the same, which is what a continuation patent implies, and has nothing to do with Alice.
It's one thing to have a point, but the EFF was protesting the similarity of two patents, not illustrating how the second fell short of the Alice test, and it really had nothing to do with comments on the guidance itself, which is what the USPTO was asking for. Including protests in consideration of feedback on guidance is not how things work. I won't go into that, but there's a place for such things and this isn't it.
And I agree, EFF has a legitimate point. But this was not the way to point it out.
Legally, this is what I read:
Q: "How can we do our jobs better?"
A: "You aren't even doing your jobs, idiots."