If one were to accept one of the arguments offered in Bush v. Gore, that of equal protection, wouldn't it be wise for Congress to establish voting and counting standards for all federal offices? Why not have a separate ballot for national elections?
Federal ballots should be created for elections to the House, Senate and White House. Strict guidelines could be put in place for counting these ballots. They could be designed to make manual counting easy. Voting machines are institutionalized, so it will be difficult to eliminate them, but a parallel federal ballot, to be counted manually, would not make the machines obsolete. States can continue to use them for their own elections. There might also be a way to 'federalize' state ballots that allow them to be counted by machines but with easier provisions for hand recounting.
I agree that Federalism demands that each state establish its own procedures for conducting elections. But that doesn't mean the federal government should relinquish its constitutional obligation by deferring to the states the power to conduct its own elections. If there was ever a good reason for federal government intervention in state matters, this is it. And it can be done in such a way as to preserve state autonomy in electoral matters.