Cool idea that could work with MLS. But only MLS it seems... Reason being the fact that a football club (though it may adopt the name of a city) doesn't usually align itself with the whole of any given city. It's a club. Therefore its crest should be unique and specific to the club itself. This could be the neighborhood in which it was founded, it could have something to do with the founders themselves, or reflect the club's nickname. In MLS I understand that the teams are franchises which represent specific cities which is why, in this case, I think your idea is a good one that can work well.
