1) alternating activations (like in bolt action) where you issue an order to a unit, then I issue an order to one of my units, and so on.
2) a new characteristic value called "discipline" that is basically like leadership except it is only used for things like swift reform, staying organized in combat, shooting in extra ranks, or restraining frenzy and things of that nature.
Mainly, there should be a difference between courage and discipline.
3) simpler combat, shooting and magic. Just lessen the total number of modifiers for everything, less special rules that could be replaced with simpler rules that basically do the same thing.
I am currently 30% done writing a ruleset from the ground up that incorporates all of these changes. It should be a complete standalone game where you can play warhammer in a new way, but still have the fantasy battle aspect of previous editions.