SAs -- all of them -- suffer from 3 things when it comes to D1 football: size, skill and speed.
Let's face it . . . 99% of really good (read 4* and 5* recruits) won't go to a SA for any number of reasons. These include (but aren't limited to): not smart enough; want a chance to go pro; don't want service commitment; don't want military lifestyle; don't want to HAVE to graduate in 4 yrs.
Given lack of speed, size and skill (compared to big-time D1 schools) -- and especially passing skill at the QB position, your best chance to win is to run the option effectively AND play teams in the bottom of D1. USNA may not see the same success when it moves into a division next year.
The option disguises a poor-passing quarterback, receivers who lack speed to get open and/or beat their man downfield, and an O-line that lacks size. And, since most D1 teams don't play it, they don't practice vs. it most of the year, and you hope that they won't be disciplined enough to beat it. You also hope that, by using the ball control of this offense, you keep your defense -- which also suffers as compared to big-time D1 schools -- off the field.
USAFA plays a mixed pro-set and option (or appeared to in the few games I watched). Didn't go so well for them this year.
I think USMA's football issues are more complex than their coach or their system The option is their best bet from a football standpoint.