I'm not sure either, having never modded myself, but I figure that if each unit can only get such and such upgrades, from *here* to *there*, and also given the fact that each armor level has it's own appearance, then each armor type must be defined somewhere, and its properties hopefully are open to modification.
If there's a line of code somewhere that states "if militia is upgraded once then give militia padded_militia skin", it probably can be turned into "if militia is upgraded once then give militia padded skin and +3 def", no ? Anyone with Rome/MTW modding experience (or anyone from CA, but that's asking for much ) around to answer that kind of technical stuff ?

That's the only way I can think of to change things in a satisfying manner... While I certainly want plate-clad militia to stand fire as well as plate-clad knights, and am excited by the possibilities it entails, I do *not* want peasants and militia to withstand any kind of fire when they are buck naked.

Besides, giving naked units a base armor of 3 doesn't adress the problem of later militias that go from naked to half-plate in one go... And giving *those* chainmail-like base armor when they're naked won't do either.