They weren't ready. That's not untrue in the least.
How much of that can be attributed to players who lack the talent to stop the run and pass or to the coaches who lack the philosophical wherewithal to challenge the next iteration of NFL offensive philosophy? It's already alive and well in SF and that's why they got to play in the SB. It will always be both although I would guess that "blame" is around 60/40 assigned mostly to coaching, maybe more.
The emerging offenses of the NFL have passed Pettine by. Can there really be any doubt about that now? Pettine's defense could not stop SF and they made it look easy getting past the Packer's woefully outsmarted and outplayed D. Twice. What's troublesome is that the 49er offense was able to dictate the outcome against so very little resistance no matter what the Packers tried on D. They had no answers for either the run or the pass. They dictated both games but in different ways. Ya gotta stop something and you can't say you stopped the pass when the other team did not even need to pass to demolish you.
The latest game reminded me of the Kaepernick embarrassment. There was a TV shot during that game of Capers up in the booth. After yet another Kaepernick option for big yardage, Capers pounded his fist on the table purely out of frustration. He had no answers. None. He was ill-prepared for the option play and, mercifully, that game ended before Kaepernick could zoom to 300 yards rushing. That one was all on coaching.
It was not much different for Pettine in the last 49er game. Adjusting his philosophy to fit contemporary offenses by next season will be critical, at least if the North is not really enough. You can be sure that other teams will try doing the same things that SF did and with even more refinements than what was seen last season, especially when they play SF yet again.