The fall of Vicksburg made Grant a national hero and a political threat to Lincoln. If one remembers, Lincoln spends a lot of energy finding out if Grant is a Democrat or a Republican. He spends energy if Grant has any political aspirations for high office. Grant gets commander of all the armies because Lincoln wanted to sideline Grant...
1. Lincoln saw Grant as a political threat.
2. Lincoln put Grant in charge of the entire Union Army for political reasons, rather than because he thought it would be a good way to win the war.
3. Any parallels between how Lincoln treated Grant and how Polk treated Zachary Taylor (which is the best known example of a president treating a successful general as a political threat).