To my understanding, the USPTO is entirely aware and quite unhappy with the recent turn of events. For better or worse, it does not have much influence over how the system works, leaving the decisions to the political machinations of others-- ostensibly, well-funded lobbiers and greedy legislators. And the latter hold most of the blame.

You see, the USPTO used to be funded out of the general coffers, leaving the patent fees as a nice little christmas bonus that served mostly to keep people from wasting the PTO's time. Then, our legislators decided that it would make better fiscal sense to let the fees fuel the Office itself rather than shuffling things back and forth. But wait, there's more! The PTO only gets to charge the legislature-set rates, and then its coffers get raided for 10% of their earnings. So now the patent system gets screwed up because our Beloved Congressmen figured out a way to make a bit of money off the deal.

Thus, the PTO has to float itself off of fees-- but can't set the fees to costs, or even hold on to all the money once they've received it. This is why they have to work on a strict quota system; there's no space to make allowances for things like, say, the size of the patent application. A 20-page peanut de-sheller gets the same time as a 200-page biofuels refinery.

Oh, and if the party trying to get the patent appeals a decision? (implicitly, a negative one) That time doesn't get added to the quota. See the problem now? When they have to figure out some giant software patent (or other useless/obvious/previously designed idea), turning it down creates more work that they don't have time for. So the examiners don't have time relative to the size of the claim, nor do they get time allocated for them to go through and fight the appeal when they turn it down. The system naturally leads to allowing exactly the outcome seen here; the Office itself has merely responded to outside pressures and control.

So, if there's anybody who's been most directly screwed with the patent system, it's the PTO (and its stalwart examiners). And it's our fault, because the fundamental, systematic problems came because of greedy, reprehensible legislators riding high on massive voter apathy.