Well. You're really looking at two completely different problems. Although I suppose they're related since the reduction in skill due to armor worn kinda cancels out the benefits of wearing armor in the first place.
What I would do is the following:
1. Eliminate combat skill penalties for wearing armor. Apply them to the fatigue rolls instead and as skill penalties to specific skills where it makes sense to apply them (swim, climb, etc).
2. Change precise strike entirely. The two critical changes I'd make:
A. Aimed blow: The attacker may choose to reduce his attack skill by any amount. Each 5% of skill expended allows him to shift the location die roll by one point.
B. Bypass armor: The attacker may choose to reduce his attack skill by any amount. For each 10% of skill expended, he may ignore 1AP of the defenders worn armor (not parrying points though).
Seems simple. It's scalable to power level. Higher skilled people can avoid larger amounts of armor if they want to, or hit any location they want to. It also eliminates the "all or nothing" effect of bypass armor as written in the rules. I should not be able to spend the same 40% to bypass a dragons armor or a bandits leather. One should actually be "harder" then the other.
Of course, I'd also include the ability to expend skill points over 100% to subtract from both your and your opponent's skill. That way, your defensive skill makes it harder for the attacker to bypass your armor or hit the location of his choice (which makes incredible sense). It retains the ability for a highly skilled warrior to take on a low skilled but heavily armored monster as well (and any other situations you could dream up), without being abusive.
As the rule's currently stand, once you've got a 140% skill, there's not much benefit to gaining more (except crit chances). This provides a natural scaling that goes as high as you want it to go.