Not proof, but when Franklin hired him, he didn't want much change in offense, esp. with terminology, and was against a new offensive system being installed. KC said he would do that.
Franklin said that the offense they had planned changed with the loss of Brown and Cain. Whether he thought KC was too slow to adapt, who knows, but the offense changed later in the season. It is also strange that Franklin said after last season that the QBs needed to run less and then they ran more. A matter of circumstance or design, don't know, but KC seemed to call more QB runs than he did at MN.
Maybe Franklin wasn't all the happy with the QB development. Clifford still has mechanical issues and they weren't trusting Levis to throw. Franklin mentioned several times that Levis needed to throw more.
Franklin obviously had reasons for the change, so hope it works out and hope KC finds a landing spot. Maybe Harbaugh will hire him.