I'd be really interested in knowing if and how they changed the relationship between armour and piercing, and the way terrain bonus' worked from HOI3 (TFH) because the system used there led to some really odd unit combinations being good. For instance, you were far better off having armoured brigades spread across your divisions rather than concentrated in a few breakthrough units. Also, if you made 1xARM 3/4xMTN divisions , they would eat everything in their wake in mountains and hills, the same was somewhat true with marine divisions as well.
Theres a couple of ways round it, at least from the HOI3 system, one would to use a gradual bonus to the armour bonus rather than a on or off modifier to divisions if the enemy can pierce the tanks being used. The other way might be to change the way terrain bonus' work, in HOI3, adding say an ART to a MTN division would hold back not only the ART, but also reduce the effectiveness of the MTN in the divisions too in mountains. Instead it might be better that if attacking in a mountain, only the ART is reduced in combat effectiveness etc, but all this wholly depends on how the new division template system actually works in determining the combat efficiency of the division