Whether or not you agree with Sigi Schmid's contention that "U.S. Soccer is trying to make it difficult for (the Seattle Sounders) to win an Open Cup," we can probably all agree that buried in his statements is some truth about the lack of transparency in the tournament.
Unfortunately, the way Schmid went about making his point allowed USSF President Sunil Gulati to avoid the issue when he said "Sigi's comments are completely inappropriate and frankly quite offensive." The problem was that Schmid's comments were so personalized that Gulati could kind of gloss over the fact that Schmid kinda had a point.
That point being that the tournament has a perception problem.
On Schmid's point, it does lead to easy conspiracy theories when U.S. Soccer can decided to rework the draw at any point and doesn't make the coin flips that determine home field publicly observable. But there are other issues, too. The fact that teams often have to pay large parts of their own travel; that the league can't even maintain a proper website devoted to the tournament; that the prize money is rather paltry; that the final is usually the only game televised; the list goes on.
Hopefully, Schmid's comments will prompt a little more transparency on some of those issues. Unfortunately, nothing Gulati said should give us much hope that he even received the message.