The Zags strong armed the conference a little. For several years Coach Few has been public about the other schools needing to invest more in their programs. Several schools have hired new, and better coaches, and a few have committed money to upgrade facilities, but some (Pepperdine) reversed course AFTER THEY RAISED THE MONEY and canceled the arena upgrade (it's now back on the books again, but that was a really bad move).
So, two years ago it all came to a head when Gonzaga threatened to leave to the MWC. The WCC then resigned to having unequal NCAA tournament revenue sharing. Whoever actually earns the money by playing in and winning in the NCAA tournament gets the biggest piece, which is mostly Gonzaga. They also redid the schedule so the top teams avoid playing the worst teams during the season and in the tournament.
When BYU joined the WCC we had a more traditional bracket, but they had previously had the same bracket we have now. It made more sense with only 8 teams, but this way it protects the top teams, and the most likely team to go to the NCAA from having to play a really bad team and from getting upset and having a bad loss. It's better for the top teams, and better overall for the conference to maximize their NCAA tournament revenue.