The MLS has greatly improved the >other< CONCACAF nations. That hurts US Soccer right off the bat (see Trinidad and Tabago). The USMNT players who play in MLS don't improve which drags us down.
There was also a time when it was anathema for US Internationals to play in the USA rather than to hone their skills against the top players in Europe. That all changed when Landon, Bradley, Deuce, Howard, and others "came home" to cushy little MLS spots. There was a time when Bradley and Klinsmann both told players they would not be considered if they weren't playing somewhere other than MLS. All of a sudden, that changed. I'm guessing Sunil and Don Garber had something to do with that.
MLS now has its grubby hands in the Development Academy system. I know for the Chicago Fire, their youth team brings in a TON of money to the club. Now, about 10 years after the MLS teams got in the DA game, we find ourselves NOT QUALIFYING for a World Cup and we have a "lost generation" of players. Hmmmm.... I wonder if there's any coincidence there.
Interestingly, when the DA system began, they left the girls "out in the cold". During that time, the USWNT qualifies for World Cups, wins World Cups, qualifies for Olympics, and wins Olympics. That doesn't happen on the men's side. Luckily for the ladies, they've not got them in the corrupt and ridiculous DA system as well. When the US stops its dominance, many apologists will just say "the rest of the world is getting better".
MLS fights as hard as it can against NASL and USSL and stands in opposition of promotion and relegation. I'm not a pro/rel fan because I do believe it has unintended outcomes that doen't work too well within a land as large as America, however, the MLS contingent squashes those other two leagues.
And last but not least is the incestuous relationship of Don Garber, Sunil Gulati, Soccer United Marketing, MLS, and the USMNT/USWNT. It is a damn travesty and if the general populace cared more about soccer, it might be the biggest scandal in all of American sports.