Got a few minutes here. I've read the decision, the concurrence, and the dissent, and I mostly agree with the dissent.
You really have two issues in the case. First, is the agency required to follow the law, and if so, have they? Second, if they are required to follow the law and have failed to do so, what's the appropriate remedy?
I think everybody agrees that the agency must follow the law and has failed to do so. The statute is clear, and the agency clearly has screwed around. The concurring opinion outlines the blatant disregard for the statute that the agency's previous chairman illustrated. (After he got slammed by the Inspector General and after oral argument in this case, he resigned.)
The problem is remedy sought. This wasn't a normal lawsuit. It was a petition for writ of mandamus. Without going into a boring procedural analysis, a writ of mandamus is an extraordinary court order issued against an agency or a public official to correct clear violations of a clear duty to take a specific action. (In this case, the action at issue was to process the application.)
The keyword is "extraordinary." Courts aren't supposed to willy-nilly grant mandamus writs. (In fact, if courts were too quick to order agencies around with writs of mandamus, that by itself would present a separation of powers problem.) Accordingly, courts should abstain from granting mandamus relief unless it's truly going to make a difference. With the inadequate funding, it's not going to make an impact here, particularly since the agency technically isn't refusing to process the application but has merely delayed it pending funding.
What this really sounds like is a situation in which Congress has passed a law ordering an agency to act, but regional politics have prevented it from funding the action. I recognize that the agency previously jerked around, and I will disagree with paso in this sense. If you buy what the concurring opinion says, it's pretty clear that the agency (through its previous chairman) did act in bad faith. However, that doesn't make mandamus relief appropriate. The chairman should be removed (or resign, which he did) and perhaps prosecuted for a crime. However, the milk has already been spilled. Congress is going to have to appropriate more money. If they refuse in the face of funding, then mandamus might be appropriate.
Judge Kavanagh's opinion sucks. It is packed with vitriol and dicta, which is why the obviously less partisan Judge Randolf concurred rather than joining the opinion in its entirety. Most lawyers I dealt with who used such tones were either chick-lawyers with chips on their shoulders or dudes with small penis issues. The same thing applies to judges. They're still lawyers - just very well-connected (notice I didn't say well-qualified) lawyers. Kavanagh should have cut the crappy dicta and further discussed the mandamus issue, which he slopped through, even though it's just as important as the underlying issue.
Paso is right that the GOP is full of **** on the blocking of the DC circuit judges. If they want to reduce the number of judges on the bench, that's a fair argument. However, that's not a justification to block nominees. A court's size is changed by the law creating the court being changed, not by nominees being blocked.