I love most of what you've said. But I think that by allowing Congress to overturn the SC you'd just transfer the runaway branch from the judicial to the legislative. Essentially you'd let them get away with passing anything, no matter how Unconstitutional, as long as they had 2/3 support two years running.
Well, that's not much different than what they do now, of course. But at least, you'd have the possibility of voting the bums out as opposed to the judiciary. You have to leave the judiciary as lifetime appointments to try to isolate them from political games as much as possible but restore the intent to make them subservient to the legislature (witness what happened with direct election of Senators, as opposed to selection by state legislatures - a twofold effect of greatly lessening the role of the states in determining federal policy as well as turning great statesmen into political hacks). Alternatively, you could just prevent them from having the power they usurped in the first place via Madison v. Marbury of deciding Constitutionality.