As you can see in the above screenshot, Matt Nagy has both an offensive and defensive playbook assigned to him, so if the Bears were to change their defensive coordinator, the defensive system would, presumably, remain in place. It is possible that a team's plans could be changed due to personnel firings or hirings could be a good idea and would add a bit of variety to the user's experience.
It's difficult to accurately capture the game-planning features of football in a realistic way. It's therefore difficult to take the blame Madden designers for choosing an in-game system that has attribute boosters based on certain types of play.
A sound game plan will do not make players more adept at certain aspects of the game. Instead, it puts players in situations which allow him to perform his job more effectively through play-calling. If my top corner isn't able keep their best receiver in check regardless of what we do to focus on man coverage this week, we're probably not going to be able perform a great amount of Cover 1.
One way to make that happen more realistically might be forcing users to pare down the types of formations and play options they're required to select from in a game. So one week, when you're up against a team great at defending zones inside You might choose to play more outside zone run plays within the game plan.
This could be a way to boost the importance of your coaching staff. Having a higher-rated coordinator might permit you to incorporate more plays in the game program each week. Having a poorly-rated assistant might restrict your play-calling options. I like the idea of adjustments for halftime, and the idea could be carried into my proposed system.