Madhuri asked a great question yesterday concerning Cohens and Article III's allocation of the Supreme Court's original and appellate jurisdiction. In essence her question was this: if Marbury held that Article III defines what must be in the Court's original and appellate jurisdiction, and Virginia was a party in Cohens, and Article III states that the Court shall have original jurisdiction "In all Cases . . . in which a State shall be a Party," what gives? How can these fit together?
They can't. So the Court (and Chief Justice Marshall himself, the author of both) effectively overruled this part of Marbury in Cohens. He held (in a portion of the opinion not included in the casebook) that, although Congress cannot expand the original jurisdiction of the Supreme Court beyond those cases specified in Article III (which was the precise problem in Marbury), Congress can permit those same cases to come to the Court on appeal (in Cohens, from a state court).
Why? The basic problem is that something had to give. A state is always a party in a criminal prosecution initiated by a state. (At that time, as now, more than 90%, perhaps 99%, of criminal prosecutions were initiated by states, not the federal government.) By necessity, a criminal case initiated by a state against a defendant originates in a state trial court. Thus, such a case simply could never reach the Supreme Court of the United States if the Supreme Court could only exercise original jurisdiction over cases in which a state was a party. In other words, that reading of Article III would render every single criminal prosecution initiated by a state immune from federal judicial review, no matter the federal constitutional or statutory problems it raised.
(Perhaps such convictions could be challenged by seeking a writ of habeas corpus in federal court. But that is an indirect challenge to a conviction, not a direct appeal. Moreover, federal habeas review of state criminal convictions did not exist until the 20th century.)
Faced with this structural implication, the Court held that Congress could authorize the Court to exercise appellate jurisdiction in cases that Article III specifies as falling within the Court's original jurisdiction.
As the Judiciary Act currently reads, there is only one set of cases in which the Supreme Court's jurisdiction is original and exclusive: suits between two states. The others may be brought as an original matter, but need not be. The Court can review them on appeal as well, and it basically always does.