The thing is, I only gave +3 armor to those troops that had the potential to be upgraded. Stuff like Swiss merc pikemen and African warriors that can never, ever be upgraded I left alone. The leather tanner takes 2 turns to build and is extremely high on the AI's building list, so after the first 30 turns or so of any campaign all those unarmored militia will often be fully upgraded.

The difference between 3 points of armor after upgrades and 6 points is very great. Incoming damage is cut by at least 30%, making units such as pikemen and musketeers much more resilient, rather than constantly getting beaten up by relatively low-tech units like Italian Spear and Crossbow Militia just because the latter come equipped with padded armor (and can upgrade to heavy mail too).

It would of course be best if CA would either fix the armor upgrades or tell us why it's set up that way. It's a real pity because I really like the graphics and the upgrade system. They put so much effort into the armor levels, why did they fail to implement the actual gameplay effects?

Btw, pikemen and most militia do not get partial plate, they wear the equivalent of heavy mail, which in their case is usually a breastplate with maybe those "legplates" attached. If you compare their upgraded armor graphics with say chivalric knights, you will see that their limbs are usually unarmored, whereas the knights have mail or plate on their arms and legs. Demi-lancers also wear breastplates but no other armor, thus they only count as wearing heavy mail. If you upgrade their armor to partial plate, you get those three-quarter "lobster suits" instead, with armor protecting the arms and legs.