I really hope they keep this system. I'm running a 3 Physical 1 Magical tactician game at the moment and it going great, in fact i'd say it works better than having a pure physical or magical, otherwise you're missing out on some good abilities.
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In your "low hp no physical armour" example, it's not a problem if you give your mage necromancer abiilties, they deal physical damage, but scale with intelligence, giving your mages options to help you. corpse explosion, teleport, reactive armour are also mage skills that deal physical damage, corrosive touch affects physical armour. empalment and earthquake have physical based effects, and skills such as venom coating, firebrand and spark master rely on physical weapons to be effective. also shield bounce if you have a shield on a mage. scoundrel has 2 great skills that hurt magic armour, lizards, dwarf, red prince and beast have racial/origin skills that are magical based that'd be useless if played in a full physical party too, as well as elemental arrows, poison coating weapons, and any runes besides physical.
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Shields are great for supports to keep them up and running and the shield toss ability is great too as it only scales off the shield.


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