So lets actually discuss ways to make it a better representation of real football.
I can think of 3 alternatives to hot routes at the LOS. Moving it to the play call screen, adding a rules feature, and going a step further from formation audibles to play audibles. Conversely hot routes could not be changed and instead the developers continue the path of making gameplay more realistic so that the exploits aren't as effective.
First, moving it to the playcall screen like we are forced to do with formation subs. This is the weakest option and if the center point of your argument is realism then this is DOA. It is not realistic to make adjustments in the huddle before knowing anything about the offense's alignment. This is how you end up playing an outside technique against a WR in a plus split and the coach looks at you like you are stupid.
Implementing a rules based feature. Along with a total overhaul of the way plays are called, this is the most realistic. It would also be ridiculously time consuming and difficult. Basically there would be a team management/strategy screen where you set adjustments for each scenario you want to. This is where I would set to press/shade inside the backside WR in a 3x1 set. The problem with this isn't that hard to see -- there are a lot of scenarios. It is doable, but this is where I go back to saying the current LOS adjustments accomplish the same task easier so why needlessly complicate things.
Play audibles. Hell it may actually be the next logical step. We went from setting audibles, to setting different audibles for each formation, so maybe next we designate 3-5 audibles per each playcall. I don't like this option for two reasons, it is time consuming and I don't think it captures the finer points of NFL defenses. Madden plays on defense are not realistic on their own (previously, it is better but not there yet). I think this would be a waste of time.
If you have any other ideas for how to implement what you are suggesting let me know. Or ifyou disagree with my thoughts on any of the above alternatives we'll talk about it. Otherwise I think this conversation has run its course.