Everyone knows that BYU is harder to get into than the U of U. That's a quantifiable fact. But that does NOT necessarily mean that BYU is a better university. You have to look at all kinds of factors to determine that.
My understanding has always been that BYU focuses on undergrad at the expense of graduate programs. I've also seen data suggesting that BYU professors aren't always the most regarded due to the LDS preference (a little like the Sitake situation).
Most ratings seem to indicate BYU is a better academic institution (US News, Businessweek, etc.) but that is not absolutely the case.