If the cameras were drawn back a bit, it would have been obvious the 49er offense played as if they'd never seen 'man' coverage before and had no idea how to deal with it. Young receivers aside, the offensive coaching/game plan was inept and sophomoric against this defensive scheme. There was not much new about it, yet it baffled and crippled the uncreative 49er coaching staff, beginning with Harbaugh.
Secondly, and perhaps most importantly, Kaepernick has some growing up to do. He parades up and down the sidelines in that idiotic gangster hat, flattened brim just high enough to expose the adolescent cluelessness of a teenager. He needs to drop the affectations (sorry about the precious 'tats') and spend some time around some mature adults, not Harbaugh obviously. The coach is a child in a man's body, an emotional mutant that hasn't a clue about how to behave like a grownup and is not mentor material.
Kaepernick's floundering is going to get him injured. He clearly was told to shorten his runs by sliding early, something he does not do well. He is skilled at avoiding direct hits when he scrambles for first downs, but his current coaching (sic) has him bailing early, something he just isn't very good at.
He looked like a stork on a leash out there. He needs to mature and quickly, before his new found fame and the 49er staff gets him seriously injured.