Gregg Roman is an idiot. If he ever gets a job after losing the super bowl after retarded play calling with all the marbles on the table, I would be shocked, and feel bad for that teams fanbase. He knows how to set everything up, set the table so to speak, with formations and wrinkles etc, but when it comes down to getting first downs on 3rd down and scoring in redzone (you know, the most important things on offense) he is abominable.
edit: And yes you can blame it all on Roman. Dont be fooled by Kaepernick sending a man in motion every other play, there isnt much cadence to this offense or many audibles in conventional situations so what Gregg calls goes usually.