Mmm...yeah, I also think the skill penalty (-1 per AP) is a tad too steep. Makes no sense either.
We were considering just halving this value.
But my suggestion is to use the armour's ENC as a skill penalty. ENC, as all old-timer RQers know, reflects not just how much an item weighs, but how awkward it is as well. Makes more sense.
Of course, as others have already suggested, if armour is worn correctly then it shouldn't hinder the wearer unduly anyway. Still, this is a GAME, and as such there has to be a mechanic for penalising those in heavy armour and giving those who wish to play lightly-armoured thiefly characters an opportunity to survive. Yes, it's contrived and abstract, but that's the nature of any game that requires rules.
Anyway.
My suggestion (intent) is to use ENC as the skill penalty.