... seems like there's really no possible way for us fans/outsiders to pin this down. Looking from the outside, there may be different (or, realistically, a combination of) reasons. All we can do is speculate....
For my two cents: It seems like we want to blame RW or Shotty or PC completely. Realistically, it's a combination, right? No one can profess to know if Shotty didn't adjust or if he did, but RW just couldn't change his focus/play mid-season. ...or Shotty didn't adjust because the staff saw, during practices, more downside to doing so. ... or didn't have faith that Russ could adjust mid-season.
We all know RW has always been a preparation robot. He's had a few other things going on in his life the last couple off-seasons, but I think we all believe he's still putting in more time/prep than 99% of other starting QBs. We also know, when he was younger, his most memorable plays were a result of abandoning his pre-snap plan... abandoning his prepared play. It seems like a paradox that couldn't co-exist forever. I don't know, just speculation, but this seems like it could be a factor. If RW spends the off-season with a "Let Russ Cook" mentality and practicing/preparing more downfield plays, how does he get out of that mentality mid-season? ... or does Shotty believe it would be too detrimental to push him out of that mentality?
Of course, none of that has anything to do with the Defense. That's probably more interesting, just because you could see players making plays they missed early in the season. I think it's normal for a team to get better/play better together as the season progresses. The D did just that. The Offense just seemed to hit re-set in the middle and have to start gel-ing again.
Again, my two cents. We'll all know more when RW adds "author" to his list of non-football activities... maybe in 15 years or maybe in January...???