Even though the release and optimization of Rome 2 was horrendous, even though it intensified the DLC politic and generally dumbed down the campaign map gameplay with hollow limited slot cities, no more on-the-map-ressources, extremely gamey army limits and restrictions... well for all of it's failures Rome 2 generally did a good job with the total war engine on the battle map (after a number of patches).
The most important features are for instance the different missile block chances provided by different shields from the front (and the left). The impact damage caused by cavalry on the charge (cav mass*charge speed) which is independant from charge bonus or attack values, the different mass of different units playing into their bracing (and units in fire at will mode wouldn't get bracing to balance infantry javelins). If you charge a unit from the back they don't benefit from their melee defence (and shield armor ? not sure) and you get an attack bonus. And of course the health system which like you said reflects minor wounds but also somewhat nerfed ranged units.
All of these things are excellent game mechanics that need to be kept, improved and expanded on. Then you have stuff that if just bad or broken like the pikes that are nothing more than a glorified picked fence. In rome 2 if you throw two pike phalanx at each other they just stop a few inchs short and litterally stare at each other. Formation attack is never useful because it reduces your offensive potential while not giving you anything worthwhile. In attila shieldwalls and other static formations just reform at a random angle after an engagement and break you frontline.
To come back to Warhammer I think the health system is perfect for it and I like the fact that you have access to health independantly to the number of men standing . I think it was needed to properly implement monsters and heroes.
PS : I also wonder if your monsters and heroes will magically heal to full health after a battle or if they stay damaged and have to regain health like other units have to replenish men.