Many of these ideas are not possible to be implemented in RTW or even M2TW because of the engine

First off: Change the organization method used. Find some way to divide units into battalions and further into companies

Add officers and have them make some independent decisions on the battlefield. Make them selectable when you raise a battalion, have some good and bad ones

Realistic "general mode": The player controls only the general and has to use aides, which have to walk to a unit, to order units around

Star-shaped forts with realistic, long lasting sieges, breaches

Depletion of armies due to disease (in RTW and M2TW there aren't any soldiers who die of disease unless a plague strikes)

Roles of units (mostly implemented)
Infantry: core of army
Cavalry: supporting, infantry counter, screening
Artillery: cause casualties in mass infantry/cavalry

Infantry Formations:
Many of these are already implemented

Column:
Absorbs damage well (only front row gets hit)
Bad firepower
Fast movement
Good morale
Easy to form square
Vulnerable to artillery and infantry in line
Usage: Marching, assaulting fortified positions, attacking low morale units

Line:
Very fragile
Superior firepower
Slow movement
Holes form in line
Usage: Musket firing

Square:
Vulnerable to infantry/artillery
Superior against cavalry
Usage: Protection from cavalry