What do you mean by the bolded? Was the decision done in a vacuum?
You're ignoring the opinion of EJ's coach at the time. I don't think I've ever heard such lukewarm praise that Marrone had for Manuel during his rookie season, which concluded with a puzzling shutdown after a knee injury. In retrospect it was clear that Marrone never bought into Manuel's promise and has since been proven right. The much maligned Hackett offense functioned much better with Lewis & Tuel, because they didn't need to dumb down the playbook anymore. In the offseason, Marrone went ballistic when told that his future rested on EJ again, and the help would come from an expensive trade to get Watkins. Again, Marrone was proven right in retrospect.