The death of Daniel Inouye - all honor to his memory, pretty much the last significant survivor of the last great Senate, and also lately its president pro tem - has afforded Matthew Yglesias the opportunity to write about the absurdity of putting this purely honorary position third in line for the presidential succession.
Yglesias' points are all accurate and thoughtful, but more needs to be said. President pro tem was not originally honorary. The Vice President, as provided for in the Constitution, normally presided over the Senate, and the president pro tempore, to give the title in full, was elected just for the occasion when the VP was absent or the office vacant, to actually preside over the Senate, and was chosen for his actual qualifications to do so. So reliable was the PPT that, in the first presidential succession act of 1792, he was placed second, not third, in the line of succession.
This is why some people claim that David R. Atchison was president for one day in 1849 between the expiration of the term of President Polk and the inauguration of President Taylor. But this is not true; the president pro tem was pro tem, remember, and as Congress had adjourned sine die, Atchison held no such office at the moment and had to be elected anew to it when the new Senate convened.
The temporariness of the office is what led to a change in the law in 1886. The Vice President had died, neither house of Congress had gone into session yet, and thus had elected no Speaker nor president pro tem, so the line of succession was completely vacant. What there was continually in office was a Cabinet, and so the line of succession was changed to eliminate the Congressional officers entirely and put the Cabinet, starting with Secretary of State, in their place.
It made sense. Half a dozen Secretaries of State in the past had actually gone on to be President in their own right, while only one each of Speaker or president pro tem had ever achieved that office. (Trivia question: who were they?)
Ironically, just about that time, things were changing. The Senate changed its rules in 1890 to make president pro tem a permanent position; while he still needed to be elected at the start of each Congress, at least the post ceased to expire every time the VP resumed the chair. In the 1930s Congress began meeting just before the start of the presidential term, instead of nine months later; this eliminated the reason for the 1885-6 gap. No Secretary of State since 1886 has become President, though several have been plausible candidates for the office, including the current incumbent. But very few of either PPTs or Speakers have been presidential candidates, either: since WW2, basically just Richard Russell (before he took office) and Newt Gingrich (afterwards), not an inspiring duo.
In 1947 the succession law was changed again, to the current order: VP, Speaker, PPT, then the Cabinet. This was at the initiative of President Truman, who pointed out that, since the President appoints the Cabinet, in the absence of a VP (which was the case in 1947), the President could appoint his own successor, and Truman didn't think the President ought to be able to do that.
There were several problems with this reasoning. First, why not? If a President leaves office midterm, shouldn't he be able to leave his office to someone sharing his policy views? Even Nixon, who resigned in disgrace, left his office to a man he'd appointed who shared his political stance and was merely untouched by the scandal which was the reason for the resignation. The VP and Secretary of State would normally do so; the Speaker or PPT might not. This actually became a problem during the period of Watergate after Agnew's resignation; House Speaker Carl Albert was aghast at implications that there was a Democratic plot to change the party holding the White House.
Secondly, although the President appoints the Cabinet, they have to be approved by the Senate, and it's not nominal because sometimes they don't approve. (On one infamous occasion, a nominee lost on a tie vote; the VP, who could have broken the tie, was taking a nap and didn't wake up in time.) The President in effect appoints the VP, too; though the VP must be approved by the convention and then elected by the voters and the Electoral College, they don't really have much choice, given the presidential candidate they've accepted.
Possibly Truman was motivated by irritation at calls proposing that, since the Democrats had just massively lost the 1946 midterm elections, he should appoint a Republican as Secretary of State and then resign; but, perforce, Republicans had become Speaker and PPT and, once the law was altered, he could have resigned with the same effect without taking the intermediary step.
It's also possible that Truman saw the Secretary of State as the President's creature in a way the VP was not. The VP cannot be fired midterm as a Cabinet officer may; also, the idea of the VP as the President's choice was a new one, dating from FDR. Previously, VPs were usually picked by party bosses as ticket-balancers and forced on presidential candidates who often held very different political views. (This had created political turmoil at every midterm VP succession up through 1901.)
Ironically, things were changing again. The idea of the VP as the emergency backup President was beginning to take hold in hair-trigger Cold War conditions, and concern for the rest of the line of succession to be similarly ship-shape was growing. Meanwhile, the VP's presiding over the Senate had become more nominal and purely ceremonial (the nap incident mentioned above was a major blow to VPs' credibility as presiding officers), and so was the president pro tem's. Strangely, the last vestiges of the office's role as the best senator to preside in the VP's absence was cast off at just about the time he was put back in the line of succession, and since then he has always been automatically the senior senator of the majority party, with results that Yglesias describes. Meanwhile, the actual presiding over the Senate is now usually done by majority-party frosh, who thereby get the opportunity to learn Senate procedure. The Speaker of the House is still the leader of the majority party, but that's equally tradition: he doesn't have to be (the Speaker of the British House of Commons is emphatically not, but is entirely nonpartisan).
In the meantime, if something should happen simultaneously to Obama and Biden, who should become President? Should it be John Boehner, or, if he went in the same explosion, Inouye while he still (barely) lived, or Pat Leahy, Inouye's putative successor? Or should it be Hillary Clinton or (prospectively) John Kerry? I think the answer is obvious.