What may be "so indefensible" is, perhaps, simply a misunderstanding of what the Electoral College is, and has been for over 200 years. The President is elected by the electors of the several States--and, as Puerto Rico is not a State, just as the District of Columbia (prior to a special exception in the Twenty-Third Amendment), or just as many of the western continental territories prior to states, it is not entitled to vote for the President. The inability to vote, then, is wholly defensible if one understands the Electoral College as a decision of several States, and not simply of citizens (or nationals) of the United States.
That, of course, may raise an important issue of Electoral College reform, and whether such a system should exist. It's worth noting (for this is rather underdiscussed) that there's a very real difference between some of the more modest proposals (of dubious constitutionality, as I've written) to turn the present Electoral College into a functional national popular vote, and a proposal that might establish an actual national election for the President.
The National Popular Vote ("NPV") builds upon the existing system we have. It would continue to state-by-state elections, and compacting states would pledge to give their electoral votes to the winner of a plurality of the national popular vote, once we assembled all those state-by-state elections into a national tally. But it would not extend the right to vote for president to United States citizens or nationals living in other territories--the system builds on the existing electoral system. (It's also worth noting that some Americans living overseas are entitled to vote in federal elections through the Uniformed and Overseas Citizens Absentee Voting Act, but Brian Kalt has forthcoming article in the Brooklyn Law Review expressing serious doubts about its constitutionality and specifically citing disparate treatment with citizens living in other American territories as one concern.)
But if one were to conclude that the presidential election should look like a truly national election--a uniform set of standards governing all Americans who get to cast a ballot--one major question would be the qualifications of voters for that federal election. I've written about this in the Arizona State Law Journal, and the complications that would arise in taking our federalist system, of state-based rules for voter qualifications, and trying to cobble together a uniform national standard. But part of that debate might include a discussion as to the status of citizens or nationals living in the territories. Should they vote for the office of president in a national election? Such a reform effort would be much more significant in this, and other, voter qualifications areas than proposals like the NPV.
So while there are efforts to reform the Electoral College, then, it's worth mentioning that some rather significant issues in this area--such as the one Ms. Clinton referred to in Puerto Rico--would remain unresolved absent a larger conversation about what our presidential election system should look like.