-I wasn't exactly serious in my comment regarding friendly fire. It's just that in my games with friends, we usually try to kill each other "by accident" as much as we try to kill enemies. :p Also, I'm the type of player who prefers having to think where to aim my skills, as to not hit allies. Especially in a strategy game. But yea, it's technically a disadvatange compared to physical. Just one I don't mind at all.
-As for dodge, that was pretty much what I meant, yup. As for ways of handling immunities, besides status effects reducing resistances (which is way too low to be relevant and doesn't work through armour, except for wet), there's also Flay Skin from polymorph. But yea, not a whole lot overall.
-For environmental effects, my point still stands, I'd say. Somewhat. If fights were more drawn out and not over within a few turns (also lots of movement abilities that let's enemies avoid surfaces), the damage would definitely add up and reduce the magic armour enough to be able to CC enemies.
Also, in regards to CC-surfaces I think only electrified water/blood/etc is affected by magic armour? Ice and Oil both ignore it anyways. Well, also decay, but that's usually not an issue I think.

Also, I wasn't planning on arguing that magic is as good as physical. Sorry if it came of like that. Just that it's not as bad as people sometimes seem to think. Or rather, that it's main problem isn't the armour system. And the reverse, that the main problem of the armour system isn't it's impact on mages.