The difference, of course, is that the president and the Congress are accountable to the people. They must face the ballot box. And their mistakes are much more easily reversed, through new legislation. Supreme Court decisions, and the reliance of the Court on stare decisis, are much more difficult to reverse. And the justices themselves are totally unaccountable. Therefore, if I get to choose who gets the final say, an unaccountable court, or an accountable legislature, I'll take my chances with the legislature.
You have your wish, as far as the Commerce clause goes. The Court has upheld Congressional enactments. Get rid of the enactments, and the Courts would have nothing to uphold.