It's more then just MLS though, it's the college system, how high school kids are coached/play, how middle school kids are coached/play, and how kids are introduced to the game. It is changing with more academies opening and players going pro instead of playing in college but it will take more time.
There also is the issue with styles in different regions. The way US and Mexico need to play in concacaf doesn't translate well to playing Europe or South American teams. We aren't good enough to dictate the way a Brazil or Germany would against someone like Costa Rica so we get sucked into playing in a way we aren't good at.
It's all kind of a large circular argument. It just depends on where on the circle you want to start and push for change.