I wish we could figure that out, I know the missions really play with consistency on the football team for sure, so many coming and going. Plus balancing scholarships for kids that aren't there and ones that are in school.
The missions are actually the most frustrating part of being a BYU fan, at times... I'm happy when they go, but it sucks from an athletic standpoint. Almost all of the greatest QB's didn't serve missions (Steve Young, Ty Detmer, Gifford Nielson, Gary Sheide... plus Jim McMahon and Steve Sarkisian, granted they weren't Mormons... John Beck who's with the Redskins, and Max Hall with the Cardinals both served). Outside of Austin Collie, missions absolutely kill our skill positions. I swear you send a kid off as a Wide Receiver and he comes back looking like a Right Tackle, or struggling with a tapeworm from Guatemala. Some don't even like football as much anymore. People say missions are an advantage, and maybe for Linemen... but nobody else is too excited about signing a kid today that won't be playing for you until 2015 after a red-shirt year, and chancing his 4.3 40 turning into a 4.9. When USC came and recruited out Stanley Havili against BYU, they told him they didn't want him to serve a mission if he went there. I think the same was asked of Haloti Ngata, who didn't go on a mission, when it was BYU or Oregon (not sure though).
Basketball is even worse, we've had a whole lot of All-American High Schoolers come off the missions as so-so's or injury prone... our greatest players (Danny Ainge and Jimmer Freddette) didn't go on missions... Shawn Bradley might be the only exception, but he spent most of his NBA career getting dunked on for other peoples posters.