Regarding heroes and legions, I'd like to point out that "generals" actually did not play that big of a part when it came to commanding troops as much as marshals and stratigists. At that era, the stratigists would lay out the formations and such before the battle, and once the battle is joined, it's basically mass chaos. A battalion led by Guan Yu isn't that much more affective than a battalion led by Liu Hua, except for the fact that Guan Yu is killing a few hundred men by himself and boosting the moral of his soldiers, while the latter is hiding behind a wall of shields.
I love the existing legion system, but if you want to emphasize the powers of the "big 3" grand commanders (ZL, Sima Yi, and Zhou Yu), then have 2 classes of heroes. GENERALS only command 1 unit, making it a super unit (like the BtS Great General), and COMMANDERS can form legions with special abilities, like the HoTK legions.
For example, ZL could command, say, 5 units in his legion (can we say, 5 tiger generals?), and his special ability would be negating terrain disadvantages, and automatically hitting the units most vulnerable to the attacking type (like how Ballista Elephants hit mounted units first). Sima Yi would command 4 units, and his special ability would be, say, all archery units get to inflict collateral damage when one of the units attack, since part of Wei's tactics is to blanket the enemy with a hail of arrows.