College football has changed a ton since the mid 90s. You need speed on the field. And the one position BYU doesn't have problems recruiting speed is at LB. So why would you take a LB off the field in order to put a less talented and slower DL on the field? Bronco asked himself the same question in 2005: "Why am I insisting on playing 5 DBs when my LBs are more talented?" So he ditched the 3-3-5 and adopted the 3-4 in order to get more talent on the field.

And one more note about the 1996 defense, the two leading sackers for that team were LBs (Muirbrook & Martin). Imagine how much better that defense could've been running a 3-4.