The conferences are pretty similar at the top: Gonzaga, BYU, St. Mary's (WCC), San Diego State, Utah State, Nevada (MWC); and pretty similar at the bottom: Loyola Marymount, San Diego, Portland (WCC), Air Force, San Jose State, Wyoming (MWC). Looking at the middle of the conferences, though, the MWC is much stronger.
I'm inclined to think that schools with football programs would have a higher likelihood of winning home games against Gonzaga, but that may simply be because I see those schools' names more often.