Don't get me wrong, I love the U.S. Open Cup, and I am glad it is getting more and more attention. It's a fun event, and it lets everyone participate; it has the same kind of drama that the NCAA Tournament has.
But the Supporters' Shield is a terrific achievement - just of the opposite kind. To survive a 34-game crucible as the top rated team means a lot. I think it certainly indicates who is the best team in the league, and it's not the kind of award that gets overturned due to one bad performance, bit of luck or official's call.
And I am pretty tired of hearing about the unbalanced schedule argument. First of all, as has been demonstrated elsewhere in these forums, a knockout tournament results in much greater differences in teams played than a full season with two conferences. Second, the effect is much smaller than people would believe. Go back and look at the last several years. Which outcomes at the top of the table would really have changed with identical schedules? Probably the one the Red Bulls won in 2015. Maybe the one they got in 2013. That's it for this decade. The large majority of the time the schedule didn't determine anything.
The point being that there is room for more than one trophy worth chasing. That's one of the things that more fun about soccer. The MLS Cup is the big prize, but the other two are major awards for American teams too.