I don't really know what's going on with BYU, but I think the move to the West Coast Conference actually works out better than moving to the WAC, like they originally planned. I don't think that the WAC has a single legitimate basketball school, and the WCC at least has Gonzaga and St. Mary's has been strong of late too.
As far as leaving the MWC. It could have to do with trying to get into a bigger conference without having to pay a fee for leaving the new MWC, or it could be that BYU has decided to focus on something other than the arms race for facilities, and becoming an independent in football allows them to compete on whatever level that they're comfortable. If trying to control the spending that's required to try to become a big time program is the route that BYU has chosen, then good for them...I doubt that's it, but it could be...