Speed:
Units don't sprint anymore. Just if they use the charge ability they run to try to brake enemy line on impact. Also if they are routing they run. Run stance is now more comited to preserve stamina, deal the broken terrain and don't dislodge formations.

Fatigue:
With each level of fatigue unit performance decreases sustantialy. Exhausted units are completely weak. Shooting now causes fatigue. Units can run or fight about 8-10 minutes untill get exhausted.

Weapons:
Each weapon have his own realistic damage sistem, bonus against units with other weapons (for example longer vs shorter) and also different defense bonus. Heavier weapons perform less attacks perminute than lighter and more agile ones.

Projectiles:
Now are adjusted with realistic accuracy, projectile speeds, damage and range. slings have more range and armor piercing damage but they are much less accurate. Bows are more accurate and deal more damage to unarmored units. Javelins now have a real efective range and speed (about 30-40m distance). Units with less training have much less accuracy and range than elite ones. Each projectile is adjusted to soldier expertise, weapon quality and the inherent physics of each type.

Armors and shields:
Armors reduce a lot damage recieved and also reduce lethal blow chances. Shields have a big impact in melee and projectile deflection.

Morale:
Now morale is more dynamic. Everything now have a chance to cause a severe morale penalty or bonus(win or loose combat, under enemy fire, flanks secure, units routing, casualties...). Charges (now implemented as a separeted special ability) have a morale penalty. Sources talk a lot of charges stopping on the last moment, refusal to clash... In vanilla every melee engagement starts with a charge wich is totally unrealistic.

Charges:
In reality charges cause a lot of casualties in both sides and is a risky and uncertain result maneuver. Now charges (remember new special ability) have a potential to cause severe damage but also to recieve it or finish in a disastrous rout. Expect the worst when two units clash charging each other. Normally units aproached each other mataining formation not runnig to a dangerous speed clash. Most of times charges could lead to the formation been disrupted, officers loose command over the unit and have a lot of casualties very quick.

Chariots:
Chariots are good at skirmish and also charging weak enemies (with less armor, shields and spears) but they suffer a lot charging spears, being under fire or stuck in melee. In vanilla they perform more like a mondern tank than a bronze age chariot.

Weather:
This is one of the best implementations of this title. Some of the weather and terrain effects values were increased. Maybe you have a very powerfull bowmen and chariot army but a sudden rain makes your bows useless and your chariots stuck in the mud. What an unexpected disaster! Now weather has more realistic transitions and sometimes takes more time to chage or not change at all before the battle finishes.