I also think every piece of armour should have magical and physical on it. My reasoning is thus: It's just a plain silly idea to not have any armour of a certain type. If you're in nothing but plate, you gon' get zapped and freezed. If you're in robes, you gon' get shanked and crippled. While this is solvable by mixing pieces of armour, why make that a problem to be solved? That just makes it a trap. Instead, each piece could offer different mixes of magical and physical armour. Heavy plate being on one end with a bunch of physical and a little bit of magical, and robes being on the other with a ton of magical and very little physical. Then mixing and matching isn't about just getting a grey or blue bar, but how big it is.
As you said, it is solvable by balancing armor pieces, which I have tried to do. Unfortunately I end up with some pretty low scores for both physical and magic that way. I would like it if higher level armor items had both categories. For low level items, that probably won't be the case. It wouldn't make any sense for a pair of work boots to protect you from lightening or an magician's robe to block a sword.