ESPN is paying $18 million a year for 16 MWC football games PLUS all of Boise States home games -- so it appears that ESPN is typically getting the rights to 22 or so games (depending on the number of Boise home games), and is paying only $800,000 per game. Additionally, it also gives ESPN the rights to 31 basketball games -- meaning that per game number is even less.
Where it gets hard to compare is in how much BYU is getting from ESPN, though it seems most think that BYU gets, at a minimum, around $1 million per game; and it does appear that BYU is payed more or less based on the ESPN network that shows the game.
If I had to guess about the MWC's ESPN contract, ESPN may be valuing the Boise games similarly to what it is paying BYU. Of course, if that is true, it means the MWC games without Boise are being paid half, or less, per game what BYU does.