I don't consider Marathon the Upper Keys; mid-Keys maybe. I think of Biscayne and Largo in that regard. We liked Marathon, spending a little time off and on at Marathon Marina and a few weeks at a time on a mooring. I think Pascal's opinion is quite ill informed about Marathon, but spot on about the Bahamas. We chose the Keys during times when I had business both in South Florida or needed readier access to MIA, but didn't want to hang out any longer in S.FL. Plus we really enjoy cruising far SW FL (10,000 Islands) and it's a jumping off point for that.
Back to the Keys, Marathon Marina was the only one we ever stayed in, otherwise anchored out everywhere. The newer marina at Banana Bay in Marathon looked very nice and quiet, over on the Bay side. I note they are rebuilding Faro Blanco, but on a new site over on the bay side as well.