[I]t's worth reminding folks that the legislative branch is the first branch mentioned in the Constitution, and the powers of the House are outlined before the Senate is discussed. Scholars of this stuff will tell you that the Founders meant for Congress to be more powerful than the president and the House to be more powerful than the Senate. The proof is in the pudding, or at least in the Constitution: Congress can write and pass legislation, while the president can merely veto, and his veto can be overridden. "All bills for raising Revenue" must originate in the House, while the Senate doesn't get a special power of its own. The hierarchy is pretty clear, and makes sense: The House is, after all, the most democratic body in our government.Well...yes and no. Yes, Congress is in some sense the "first branch." I wouldn't say that the framers of the Constitution "meant for Congress to be more powerful than the president." I think a better way to think of it is that they believed that in a democracy (they called it a republic, but I've been convinced that it's best to think of those terms as synonyms in most cases), the "democratic" parts were apt to dominate -- and that therefore a guiding question of the Constitution was how to restrain representative bodies chosen by the people. Their problem, as they eventually realized, was that in America there wouldn't be anything with which to constrain democratic institutions. There would be no aristocracy, or crown, or offical Church -- no other Estates. Eighteenth century doctrine followed Montesquieu and insisted on a balance of powers, but in America there was nothing to balance. There were no Powers ; there was only one power, the people.
I think there are two ways to interpret the Constitutional solution. One is that the framers somehow managed to create something other than the people -- that the (original, at least) Senate and the presidency are somehow less democratic than the House, and that the Constitution is all about constraining democracy. That was, more or less, the anti-federalist argument at the time, and it's been a popular interpretation ever since. In large part, the Federal Papers are a response to this argument. There are lots of very defensive essays about how the president isn't going to be a king -- No Really! He has hardly any powers at all! -- and the Senate isn't going to be an aristocracy, and so on.
I think a better interpretation of what the framers were up to, however, is that they realized that in America there would be nothing other than the people, but that institutional design could still achieve the benefits of balance of powers by duplicating the people into different parts of the government. Even in their original forms, that interpretation argues, the Senate and the presidency (and, perhaps, even the courts) are just as democratic as the House of Representatives, because they ultimately depend on the same constituency: the people. Yes, election was indirect, while election in the House was direct, but that's not nearly as important as the obvious fact that ultimately it all comes down to the same electorates. From the very start, there was nothing of the House or Lords or the Roman Senate in the United States Senate. In that sense, both the Jacksonian idea of the presidency as the people's branch and the eventual decision to remove the indirect election of Senators and (mostly) the president are contained within the original idea of those institutions. They always were intended to be democratic.
Why, then, balance of power? Two reasons, one familiar and one less so. The familiar reason is Madison's in Federal 51; everyone, even the people, need constraints, and separated institutions sharing powers (in Neustadt's wonderful phrase) is the way to do that. Ambition checks ambition, and so on. And that's fine as far as it goes. It is a mistake, however, to see balance of powers as purely a negative force. Mixed government is powerful -- Rome was powerful -- because each element adds something to the mix. So we can turn Madison's "ambition must be made to counteract ambition" around and emphasize not the "counteract" part but the creation of power -- the creation of lots and lots of ambition, seen in this sense as a good thing, a creative energy. As Hannah Arendt argues, power is not a zero-sum game, and one can argue that the American system is especially good at generating lots of power.
So which is the most powerful branch? That's not a question that the Constitution answers. Yes, the House is given some Constitutional advantages (revenue bills, a Speaker, direct election), but so is the Senate (more control over the executive and judicial branches through nominations, long terms), and so are the president and the courts. Each branch, and each House of Congress, can throw down roadblocks; each branch, and each House of Congress, can also innovate and initiate action. I would say that Ezra is wrong in concluding that "the House is less powerful than the modern Senate and Congress has taken a back seat to the president." It's true that, as he says, attention is focused on the Senate, but that's not the same thing as the Senate having the most power. Indeed, to the extent that the Senate is unable to act, it becomes a weak player in the system. As for the president, we're accustomed to attributing policy changes to the White House (see for example here), but that's mostly convention and simplification, not analysis. What I would say is that the Constitution gives plenty of opportunity to a shockingly large array of actors to create policy, while leaving the outcomes of their efforts largely undetermined by formal rules.
I feel like I should add a few footnotes, or at least references...I highly recommend Gordon Wood, The Creation of the American Republic; William Lee Miller, The Business of May Next; and Hannah Arendt, On Revolution.