From what I have seen:
The defense started out pretty good. But as Glennon floundered, the defense slid in response, especially since they were spending more time on the field than the offense. Then the quarterback switch to Trubisky and the defense perked up again. One aspect I have seen over the years is whenever a player has a flash of brilliance, the coaching staff eventually reels that player into how "they" want things done. Trubisky starts off his career: scans the field, finds nobody open, and takes off running. Or bootlegs and throws all over. But now he appears more restricted to the pocket - he is taking more sacks. Yes, he still has his moments of running, but he seems hesitant. The same for Jordan Howard - first year, finds an opening and bruises his way through for yardage. This year appears, "This is the play and you will run the play as it was designed." Howard slams into piles and hopes for the best. Only Cohen still seems to think on his own and makes something out of nothing.
Anyway, it appears to me the defense again has slid in response because the offense seems more handcuffed now. All those third down conversions the 49ers were making appeared very similar to how Peyton Manning beat the Bears in the Super Bowl - throw just beyond ten yards down the middle and the gap will be there. The safeties play deep to avoid getting burned. The linebackers play close to avoid the run. The coaches have changed, but the style remains.
And the players are checked out. Watching John Fox on the sidelines is like watching an old man walking towards the bathroom, confused whether he already has or will shit his pants...
