I have found that with D. Hunter as a capable Corps Commander (generally good, active more than McDowell or McClellan), the Union is overly effective in the 1861 Campaign. Since you can organize an Army HQ, and a Corps HQ, there are very few stacking and command penalties faced by the Union. As the Human Player I quickly re-organize this force into a balanced 4-Division command, 2 Divisions with McDowell, 2 Divisions with Hunter. This combination is extremely effective against the Confederates as I have lost very few battles with this force (due to Hunter being active around 75% of the time).
I think that it would suit the situation that the Federals were in better if Hunter was a one-star General, forcing the Federals to keep their divisions in individual formations, or heavily stack McDowell, or wait until one of the three star generals is free to form a Corps. This way, you have to bloody your divisional commanders to get experience and promote one of them. Historically he was a Brigadier general in early 1861 (so was Tyler, who is rated at 1 star), so demoting him does fit.