sorry, haven't been keeping up totally on this, but i have a few questions:
1) have you thought about having an overall tourney, instead of single elimination?
basically, everyone fights 3 matches against each other opponent, the highest win% goes on, tiered for maybe 12/8/4/2 or 12/4/2...that way you get to see which mono is actually best, not just which is best against its counterpart.
2) are you still allowing upped cards? if so, does everyone have access to entire upped decks? if not, then maybe everyone should be given a new account only for this competition, each having 6 of each upped card along with 20 or so towers + upped others...otherwise maybe everyone should use un-upped cards only.
These would even out the playing field, as you want to know which element(s) is(are) best, not just who has the best cards in their stock. However, it still doesn't account for bad play, but there's really no way to stop that.