I also believe that there were two personal factors in Michael's decision to remove Tom as consigliere:
First, Tom was Vito's choice for consigliere after Genco's death--not Michael's. Given Michael's ultra-controlling nature, I don't think that anyone could have served as his consigliere except Michael himself. He served as his own consigliere.
Second, as Michael told him, "You're not a wartime consigliere." I think Michael felt that, as a non-Sicilian, Tom lacked the "cunning" (Puzo's term in the novel) required to be an effective consigliere. I also think Michael held him partly responsible--justly or not-- for Sonny's death by failing to see that Carlo would betray Sonny. In the novel, Tom himself concludes, after Sonny's murder, that he's not "a wartime consigliere...old Genco would have smelled a rat."