The less populated states are not a "rotten borough" problem. For that, you'd have to have literally an uninhabited state that still got to "elect" two Senators and one Representative.
What we actually have is states that get to elect two Senators, even though they have much fewer people than other states that also get to elect two Senators. It's that way for a reason, and that reason still makes some sense in 2017.
I'd say we suffer far more from the opposite problem: Parts of the Constitution that have not been repealed, but which are no longer in force because various court decisions have gutted them. (The Tenth Amendment comes to mind.)