49ers fall was largely due to Baalke and the collapse of the defense during the post season.
Kaepernick was a decent QB. His running ability allowed the 49ers to pick up large chunks of yardage and consistently win the field position battle with Andy Lee. Then the defense went to work and the indomitable Frank Gore put a stamp on a lot of games that Harbaugh Niner team won.
It was a great formula, until Baalke started squandering picks on rehab projects and outright busts. This greatly hampered their depth during the 2014-2015 season as well as the following year.
Then for some reason, the defense couldnt get off the field come playoff time. They were able to still win some games (people forget how fucking good Kaep was in the comeback against Atlanta) but they had to dig themselves out of a hole almost every time.
The special teams also gave up big returns leading to even more pressure on the offense to keep up. Kaep very rarely played with a lead. I think it started when Bowman started to slow down. Patrick Willis and Bowman were two of the best inside linebackers of all time, it was an incredible time to be a niner fan when that defense was fucking people up. Aldon Smith was racking up sacks at an historic rate, Eric Reid was serviceable and Justin Smith was the anchor. But then all of the sudden they couldn't stop anyone and was giving up 30 points a game.
When Bowman blew out his knee after making that incredible play against the Seahawks, that was the end of that Niners team.
We have been lucky with linebackers though. Foster was a huge bust, but Fred Warner is an All Pro type player IMO and will be a perennial pro bowler and difference maker. With Kwon Alexabder next to him he is just gonna get better. Richard Sherman is back to 100% now, and they added Ford and Bosa. If this defense isnt a top 10 defense this year, Vic Fangio deserves even more credit for what he did there. There is no reason outside of injury that the 2019 49ers wont have a stellar defensive unit.