Well the armor penalties were based on what they thought the armor was like. In practice, full plate is a category of its own, since it was all properly molded and fit so that it was more like a heavy second skin. Every joint you need is articulated, and thus provides most of the degrees of motion needed. In contrast chain/ring/scale mail was fully flexible and thus applied their weight pretty much everywhere when you moved, getting in the way.
Certainly it was less mobile than wearing loose clothes, but I believe it was supposed to be less encumbering than having a 50lb backpack on you. Its not exactly representative of its armor category though, given that each suit is a work of engineering.
Armor granting hardness(though instead of setting the goalpost at 1 minimum damage, you might want to make it a formula of level) does count for a lot. On the surface it does not look like much. You take maybe 5-10 points of damage off a monster's 40 damage attack, but when you have 100 hp, and the monster is getting 3 hits per round, those points would be what makes the difference between dead, and nearly dead(at which point you have profited by a whole round's worth of counter-actions). Its like AC thats only effective against secondary attacks, it doesn't prevent the whole thing, but it does make the difference between surviving one round and surviving three.
Also I went and did the math to bang out the
Class Defense Bonus. The concept at the time of posting was to make up for the majority of
paid AC, keeping the values in the normal range but not the cost(which is zero'ed). One incidental discovery is that the working range of numbers is actually rather small, it does not take much to make a character completely unhittable to 3/4 BAB melee attackers using casual optimization(the usual maxed primary attack stat with their BAB gap(and probably dualwielding) isn't going to breach full plate and shield with +BAB to AC except on a 20), so just take the cost off the misc bonuses, make it look tidier, and free up the cash for them to buy other defenses on top.