While I'm sure part of it is Tyrod missing the crossing routes, I believe part of it is also simply Roman's offense. Based on the chart from Wraith EJ and Orton both threw over 50% of their throws to the middle of the field. So far this year (small sample size) it appears Tyrod's breakdown is 40% Left, 32% Middle, 28% Right based on the chart. I looked at Kaepernick's splits from 2012-2014 to see if it compared at all. Overall over those 2.5 years of play Kaep broke down at 30% Left, 39% Middle, 31% Right, and the highest % of attempts to the middle came in 2014 at 42%. I think Roman just tries to utilize more of the field.
Under Marrone/Hackett:
EJ: 22% Left, 51% Middle, 27% Right (Either 306 or 437 Attempts, not sure which Wraith used)
Orton: 22% Left, 54% Middle, 24% Right (447 Attempts)
Under Roman:
Tyrod: 40% Left, 32% Middle, 28% Right (137 Attempts)
Kaep: 30% Left, 39% Middle, 31% Right (1082 Attempts)