I want to say it's mostly Kaepernick. Alex Smith had the same offense, albeit with less read option stuff, and I find was a bit more efficient. Obviously he wasn't as explosive, but I feel like he sustained drives a bit better than Kaepernick. But let's not make this an Alex Smith thread.
I feel like Kaepernick is still limited by his mental ability. He can make all the throws, he can extend plays, but he's not quite there yet in reading defenses pre and post-snap. There were so many instances where I was thinking that he could have just dumped it off to a runningback or an underneath option and that would've put us in a shorter down and distance.
But onto Greg Roman... I feel like he's limited the offense for Kaepernick, but he needs to adapt to Kaepernick's flaws. Kaepernick needs to know what his checkdowns are. Kaepernick needs to know what his hot reads are. Because it feels so much that the problem isn't with our wide receivers not getting open, but Kaepernick and the scheme.
If defenses are gonna double Vernon Davis or Anquan Boldin, use them as a decoys and give Manningham, Baldwin, McDonald, and the runninbacks opportunities to win underneath. I think we just don't have the short passing game needed to supplement the play action pass when our running game isn't working.