Was Marshall even as popular as MacArthur or Eisenhower in that time period? Whenever there are lists or who would make good presidents his name keeps popping up.
I realize he was important in the US war-effort but he was no battlefield commander as MacArthur or Eisenhower.
Marshall had begun unveiling the Marshall Plan and was named the Person of the Year by the end of 1947. While he may not have been as popular as other generals, being used mainly for administrative purposes back in the states. Didn't keep him from being the front-runner to command Operation Overlord though.
Anyway, his one major flaw would be his refusal to recognize Israel as a nation, when nearly everybody else did. He got in quite a feud with Harry Truman over this, threatening to vote against the President if he did so. That doesn't mean he wouldn't later, since it was largely based on the fear that Israel would destabilize the Middle East, but it would mean he would take a more neutral path, with Israel largely depending upon Europe for support.
Korea would also be interesting. Marshall would likely have returned the United States Military to a level of readiness that was somewhat respectable, meaning we can better deal with the North Korean Invasion of South Korea. He basically gave MacArthur a blank check to do whatever required to bring North Korea under their control in hopes of uniting the peninsula. That doesn't mean that China would be carpet bombed with nuclear weapons, but there is a good chance that the armistice line would be much farther north than it is in OTL.
As for McCarthy, that is likely going to be one of the ugliest scenes to ever unfold in the political arena. He basically blamed Marshall for allowing China to go Communist, though not entirely on purpose; that he was not fit to command.