Beats me. By the time Kyle got to Atlanta, he was probably Ryan's fourth or fifth coordinator. Ryan was Kyle's umpteenth QB. Personally, I think it was just a matter of the right coach being with the right QB at the right time. Quinn's single biggest error was bringing in a quality OC in Steve Sarkisian and instructing him to run Kyle's offense. Sark's offense would have been successful in Atlanta. You can't expect a coordinator to run another coaches offense because he won't have the experience to know when to call certain plays. It was unfair to Sark and the team.
And then, he brought in Dirk Koetter and told him to run Kyle's offense. Results were absolutely dreadful. Koetter has similar plays but tweaked them until they were neither Kyle's offense nor Dirk's. For example, Kyle ran an outside zone running scheme and Dirk ran a power rush offense. We didn't have the running backs or offensive linemen to run Dirk's offense. I knew it wouldn't work as soon as I heard Quinn wanted to run the same scheme. He should have hired McVey or Matt LeFluer, who were Shanahan's disciples.
I never thought the Niners were going to draft Jones because prevailing opinion was that he'd be available later. I do believe that Jones would have started the season over Jimmy G. If Trey Lance is a guy that Kyle thinks fits perfectly within his system, he shouldn't have swept Kaepernick off the team. Lance has a stronger arm, but he's not a more dynamic athlete than Kaep was and he probably won't ever be the leader that he was.