PLEASE: no +skill equipment!!
If the penalties could be implemented into weapon proficiencies instead of skills that that is the best thing to do. Otherwise, a moderate -skill is fine and my measure for "moderate" is significantly smaller than the typical values you would have in these skills - it is important that it does not lower the skill to zero! Beyond this point it means that skill points do not matter anymore.
Penalties to power throw make a lot of sense - you will NOT throw a javelin as far when wearing chain as when you are naked (not talking about accuracy) - but the difference is not huge. A large shields is a very bulky item. Even when slang on the back it is still annoying and will interrupt with anything that require a lot of free body movement. Unlike with armor, with the shield you have the option of dropping it anytime to run faster, fight more agile or... run away - the Spartans regarded returning from battle without your bulky hoplon as a sign that you ran away.
The major point: heavy armor must be worth it!
With the current damage of weapons, stats of armor and armor soak/reduce factors, the heavy armor is not that effective in protecting you. There are 3 options (not mutually exclusive):
1. Change weapon damage on items
2. Change armor values on items
3. Change global soak/reduce factors
My personal view is that:
#1 needs a small reduction - 80% of the current value sounds like the ballpark. If this is lowered too much than even naked people will not drop fast. The typical damage of a sword (all factors included, PS, weapon proficiency, a bit of speed damage) should be about the typical hit-points of a troop.
#2 Because of the way armor damage reduction works, extremely high values are problematic. 65 (Wolf lorica) is EXTREMELY high and I would normally not go much over 50.
#3 After some testing I firmly believe that this is the key to a good damage balance. Keeping the base damage high enough to satisfy #1, but making each point of armor counting more keeps weapon deadly against peasants, but allows heavy troops some "staying power". It is also very easy to tweak since these are global factors and do not require editing module.py files.
My current values as an example:
armor_soak_factor_against_cut = 1.0
armor_soak_factor_against_pierce = 0.85
armor_soak_factor_against_blunt = 0.3
armor_reduction_factor_against_cut = 1.0
armor_reduction_factor_against_pierce = 0.3
armor_reduction_factor_against_blunt = 0.85
These mean that the defense against pierce is mostly (no only) a flat damage threshold (to penetrate), but most of what goes through the armor soak-defense is delivered as damage. It makes thrusting weapons really benefit from extra damage bonuses and weak thrusts suffer even more. Blunt weapons will produce very few glancing blows (always do some damage) and most of the defense against them is the percentage reduction (cushion effect). Slashing weapons are both effectively resisted (need to cut all the way through the armor) and reduced (need to keep cutting through the armor to widen the wound) - fighting "chain" (essentially just the top armors since the game does not make a difference) with a sword becomes difficult unless you have a lot of damage boost factors. The wolf lorica suddenly seem attractive even with the huge -4 to skills.
At the same time, against pajamas all weapons tear through them for a 1 hit kill due to the high base damage.
Your mileage may vary.