I would love to see the conferences realigned but it's just never going to happen in this game.
Realignment is incredibly fluid. The alignment that you hear about is changing every 2-3 years. However, that's just FBS and some FCS movement. Division 2 and division 3 conferences actually change quite a bit. Sometimes, you'll even see a school start a football program and then abandon it within 10-12 years. If the game attempted to keep up with actual realignment, it would be complete chaos.
I don't know a ton about programming but from what I've heard, it would actually be very complicated to adjust the current alignment because of how the engine generates the schedule.