You are wrong on so many levels, I don't even know where to begin.
First of all: Elder and X will likely have a chance to make it to state by actually playing. You have to beat the best to win state. No sense having 3 GCLS teams in the State Tournament. If you wanted to do it in this format just crown the Elite Champion the State Champ.
Second: Moeller and Darby are on opposite sides of the bracket this season. Did you even see the opening post. At any rate, this has only happened a handful of times it isn't as big of a deal as you're making it out to be.
As for the 2013 semifinal, the 2nd best team in that Bracket laid down for Darby in that match. Darby had their way and did whatever they wanted. Elder while undermatched gave them a tough/better match in the State Final.
I understand the argument, there are different ways to do it but this is what we have. It isn't broken at all, so I see no need for a fix. The points above sound very much like sour grapes which is definitely no reason to make a change.