I was under the impression that Kirk's lie on the report was the problem. The fact that this indicated to Pike and the other admirals --but mostly Pike I suspect--that Kirk was not responsible enough to own his command decisions and that perhaps his command crew did not work well together. They needed more experience. The fact that both Kirk and Spock were still going to serve in a command crew position indicates to me that it was felt they needed some training but were thought capable officers.