I want to start right out by saying that this is speculative. That said...
Matt Yglesias once again highlights what he sees as a disfunctional aspect of the US governing system, in this case all those unconfirmed political appointees. He's certainly correct to point to the problem; it's a disgrace, and one that I think Reid and Obama should have been more aggressive about (especially in fall 2009, when the Dems had 60 votes in the Senate.
Yglesias, true to his Europhile heart, believes that the real solution is to convert a lot of what are currently political appointees into civil servants. I disagree. I think the American system of a relatively weak bureaucracy that is responsive to both the president and Congress is an excellent democratic institution, especially fitting for such a large and diverse nation. It's a really good thing that a Senator from the Dakotas, or from Georgia, or from Oregon, can find ways to get the attention of government agencies for particular, perhaps narrow, needs of her constituency. The confirmation process (along with oversight hearings, and the budget process) is a useful part of that.
Or at least it was. Because here we get into the main topic of this post. It seems to me...and I do want to point out that this is speculative, but I do think it's true...that the real disfunction that's going on is that the Gingrich-DeLay Republicans discovered a ways back that a lot of the ways that the American system of government rest on norms that everyone follows, and that by exploiting the actual underlying rules players can do all sorts of disruptive things. For example, it's been the norm for almost a century that states do redistricting every ten years, after the census. Tom DeLay realized that there was no such rule -- and had the Texas GOP do an extra redistricting as soon as the balance of power in the legislature changed, without waiting for the next census. There are several other examples (using the moribund recall provision to knock out a governor in California, for example), but the big one has to do with governing the Senate. Senators learned long ago that a multiperson filibuster was essentially unbeatable as long as the filibustering Senators wanted to keep it going. And there's a very good defense of that practice grounded in democratic theory, having to do with the issue of intensity: as Robert Dahl discussed long ago, in cases in which an indifferent majority opposes an intense minority, it is unlikely that the correct democratic outcome is a simple majority vote. Filibusters, used by intense minorities, are probably a good democratic practice.
But Bob Dole in 1993 realized that there was nothing in the rules preventing the minority party, if it chose to do so, to filibuster every major initiative. And Republicans in 2009 took that one step farther, filibustering (including the use of holds) even measures and nominees they supported, just to put the president on the defensive.
In sports, if one side finds a loophole in the rules, they get a temporary advantage as a reward for their ingenuity -- and then both sides have the same advantage, and then the rules committee goes about rewording things so that the intent of the original rules is restored. Unfortunately, in politics, that sort of thing is often impossible. It turns out that a lot of political regulation has to be done through norms, not formal rules; the game is too complex, and the rules too difficult to pass, to do anything else. Moreover, because the rule-makers are also the majority party, we really don't want the rule-makers to constantly be changing the rules (because they'll do it unfairly, to their own advantage).
I don't think there's much of a solution to this. I happen to believe that the short-term gains Gingrichism sometimes gives the GOP are illusions, but they firmly believe that it worked in 1993-1994, and that it's working now, and so it's just going to get worse. Newt Gingrich in the 1980s believed in destroying the House of Representatives in order to take it over; Republicans now appear comfortable extending that to the Senate and the executive branch of government. It's a bad business.