I think the system is relatively fine and in some cases it ecourages the cooperation between mages and physics (e.g. you can use Firebrand on your party to melee the enemy's magic armour, or make your mages use necro or throw shield to damage physical armour). However, it does limit the number of options and party compositions available to the player (what if I don't want my mages to throw shields?)
My solution would be reworking hard-cc abilities to deal a lot of damage to the corresponding armour type. E.g. I want to freeze the target, but it's protected by armour, so instead of freezing it the ability would deal a lot of MA damage. This will increase tactical variety (you can quickly strip the opponent of the armour by cc abilities to kill them quickly by direct damage or you can use damage abilities to cc them afterwards) + make cc abilities more relevant. Soft cc, like shock and oil should go through armour and stack, every 2 or 3 stacks it can become hard cc (or just exploding for a standard hard-cc damage on the enemies' armour if they still have any).