Don't see how you conclude he made things too complicated or wrong adjustments. Look a the two Arizona games for example. He did the same thing both times as Fox admitted that they didn't double Fitz the first time and didn't the second time as well. Both games he had over 100 yards, the second without Boldin there.
What adjustments did he make?
Secondly almost every analyst I heard for example in the second Arizona game felt our defensive plan was too vanilla and simplistic. It was easily countered by Warner and their offensive scheme by for example moving Fitzgerald to various positions on the field. Rather than one defender moving to cover him like Gamble, we just allowed them to dictate the matchup and situation which make a completion almost a formality.
All year we have failed to stunt, give multiple looks, or try and confuse the offense. When we blitz we usually show it right away particularly up the middle and then fail to change the look even when the offense cals an audible. We routinely get beat in the very spot we just vacated when we blitz because we leave large holes in our zone.
The idea was to simplify responsibilities not our looks and schemes and it worked early. As we went to more of a zone look and played better passing teams with better quarterbacks and offenses we were routinely exposed.
I contend that Trgo has relied on our front four to overpower the opposition and when that hasn't happened for the past few years we have failed to develop more deceptive schemes to confuse the offenses we have faced. We have failed to give any more than a vanilla scheme with obvious blitzing elements easily counteracted when we have become desperate or gotten behind. When we are ahead to give them a bend don't break philosophy which allows them to march down the field, develop rythym in their passing game, and control the clock and game management.
As for what happened from the bye on, I really think in the first half of the year we focused on stopping the run with frequent five man defensive lines sets, run blitzes and had a more aggressive defense as a byproduct. After the bye we faced a majority of teams with good passing attacks and suspect running attacks (except for the Giants) and we went more vanilla and zone to slow them down. As our offense improved we also could score points and didn't have to be as aggressive so Trgo relaxed the reins and played more of a bend don't break scheme.
This is the biggest problem with our scheme and it is about to get worse with Peppers exiting this offseason. Trgo doesn't ever get pressure with anyone other than the front four and maybe an occasional linebacker or DB. I have seen him blitz marshall or Godfrey out of nickel sets...sometimes it works sometimes it doesn't (the latter being the case most of the time).
But what is even more mind-boggling than Turdo's over-reliance on the front four is what you just mentioned as a "vanilla defense." It is not just vanilla in that we always play zone...its vanilla in that its so freakin predictable (especially on 3rd down).
3rd and 8-10 we blitz a DB
3rd and 4-7 we drop back in zone
3rd and short we blitz the LB
And its like we have designated blitzers...its not like the Eagles where anyone can blitz at any different time. With our blitz its either going to be Godfrey or Marshall off the edge (they are already standing on the line of scrimmage showing blitz beforehand so it confuses nobody) or we have Thomas Davis coming up the middle on a delay or off the edge at the snap (once again standing at the LOS which confuses nobody).
I fully expect to see the exact same BS next year with very little changing except for the fact that we will get NO PRESSURE without Peppers unless we pick up another lockdown corner that people are afraid to throw at. Then we could be lucky and get a coverage sack every once in a while.