My guess is that those are actually the teams you're least likely to have a lot of fans of. LA, NYC, and Boston all already have massive and influential sports teams. The folks likely to want to watch/know about MLS are in the cities that don't - Kansas City, Austin, to a lesser extent Atlanta or Portland.

MLS is being fairly smart with its expansion and focusing on cities where they're not trying to pull fans away from the NY Yankees or the LA Lakers or whatever. Sure, they still have teams there as well, but the die-hard fans are going to be in the towns where folks are happy to have any team to be excited for.