Tom had never been through a war, and was completely untested.
No doubt he was a god lawyer but the trouble was he learned what he learned from Vito, not Genco. The idea of a consigliere and his boss also having what amounted to a father-son relationship is a bad one to begin with. As he confessed Vito had a "sentimental weakness" for his children, and this extended to Tom. The appointment of Tom was, in fact, a sign the Don was slippin.

Hard as he was on Tom, Michael always maintained he was an excellent lawyer, but as he pointed out to Kay he was not a Sicilian. There was a place for Tom in the family business but probably not as Consigliere.