What else would you have them do? They used the conference championship as a factor one year and everyone complained, they use a rating system and the same complaints - it is what it is. Losses to Nandua & WP, the team had their best players. Fact is, they didn't come to play every night and their rating suffered.
My only suggestion for improvement would be that they use a combination of rating system and conference tournament results - tournament champs get top 4 seeds & use the rating system to determine those seeds, then use the rating system for the bottom (conference runner -ups). I don't know how much that would have changed the bracket though?