I find two major, somewhat related issues, at stake here.
One is: what is the appropriate penalty for wearing armour that feels intuitive, feels like it reasonably simulates reality, is balanced in game terms and meets the criteria of MGF "maximum game fun".
The other is: is the game rule that allows you to take -40% to your skill in order to ignore armor a good game rule.
Armor penalty. I must admit that any percentile modifier that is not a multiple of 5 or 10 is undesirable especially if it is applied to every single dice roll in combat. By the time you've had to add up 68% +/- various other modifiers and then a 24% negative for wearing armour you've had to do too much complex math. My personal preference is is for amour to be tied into the fatigue rules. I could see two modifiers though:
- Helms that restrict vision might give -5 or -10% to combat skills
Wearing unfamiliar armour might be -5% per location until you've had a chance to get used to it. i.e. if a PC picks up a big magical breastplate and puts it on then maybe he should have a -5% modifier to represent not being used to the awkwardness of it.
The armor bypass precision attack is, IMHO, overpowered. It works OK up to around 100% but will break quickly thereafter. It seems to me to be more of a legendary ability that you can gain with a specific weapon skill and still gives you a minus. It could also be an option for criticals: if you roll a critical you could be given an option of ignoring armor rather than doing maximum damage.
In general I think the game could be more creative in use of penalties. E.g. I don't like being able to specifically aim for a location but you could say:
Aim high/low or aim left/right. to do so you spend a Combat Action "aiming" and attack on your next CA this round. If successful you can roll d20 as normal but if rolling high add 10 to results of less than 10 and vice versa if rolling to aim low.
Or you could aim for a specific location but only if you spend 2 CA's 'aiming' i.e. you can't do it unless you have at least 3 CAs in the round.
Other 'skills' might be: spend a CA feinting (i.e. not making an attack) so that your opponent is -10% to his next reaction against you this turn.
Spend a CA delaying so that when your opponent attacks you make a simultaneous attack preventing either of you from reacting to the attack. Classic technique for the person who trusts his armour.
Basically, I think the game needs to reduce the number of penalties for special combat maneuvers that are +/- modifiers. I've run a lot of RQ in my life and find that as players get more experienced they tend to do things that need more modifiers and the game slows down just a little too much.