I really think it's unavoidable and only going to get worse. With the "power teams" consolidating into fewer conferences, it's bound to happen. Those top teams are going to play each other more often and the lower teams are going to end up playing each other more. The TUC seems to me to be the best way to do the comparisons (albeit they might use KRACH instead of RPI). With the future landscape of college hockey, I don't see a way around the comparison system that is still objective.
With that being said, I think MSU and BSU are going to be very important to the new conference as a whole. We all know that those non-conference games are big for everyone in the conference. With the way things are setting up, it seems like MSU and BSU are going to be going up against NCHC and BT conferences more often than most of our conference mates. That's not to say that the other teams won't get those matchups at all, but with the MN Cup and other in-state series it seems like we are going to have a lot of comparisons resting on our shoulders. Maybe I'm reading it wrong, but it seems like it's setting up that way.