A pro style offense is difficult really dominate with in this day and age. Most of the programs that run it effectively (Alabama, Wisconsin, Stanford, Michigan State, etc.) have a lot better talent than BYU and even they are not know as offensive juggernauts. They're defensive powerhouses who offense just has to score enough points and not make mistakes.
I just think when BYU was at their greatest it was because they were doing things nobody had ever done before. They were David taking on Goliath. We're just not good/deep enough to go toe-to-toe with the Goliaths and win consistently. Just my 2-cents.