there is no fixed scale between scenarios, and probably not within scenarios. Some battles have Brigade sized units, other use Divisional or even Corps strength units.
Personally, I think BattleCry works best at a Brigade scale, but there is no requirement.
Similarly, terrain has no specific scale, nor does it follow map scales. So a large wood might become a strip of woods, that blocks LOS and stops movement, but is nowhere need as extensive as the map depicts.
Special rules reflect some specific character of the battle, but I agree that they shouldn't be over used. Green troops for example. Just because they are Green, if they didn't run in battle, does it matter?
Something that might be useful is set of stock phrase Special Rules. Rather than having slightly different wording for Horse Artillery or Green/Veteran troops, or Sabres hitting only in Melee or common used Special rules.
"The war is over — the rebels are our countrymen again."
(U.S. Grant after stopping his men from cheering Lee's surrender at Appomattox Courthouse.)