The initial mover is different. The arrow carries the strength of its power source; and bows are stronger than arm muscles. One solution to the bullet issue is to permit that gunpowder imparts a stronger initial mover than a bowstring. However, the shape of a typical early bullet (a ball) works against it. The first cannons were armed with spears...
Mark
Perhaps you would reach your goal by making firearms ignore a fixed percentage of the armor's soak bonus rather than substracting a fixed number?
that would still make more armour a desirable thing.
IIRC what happened with bullets is that they ignored the steel protection suince the bullet pretty much could tear a hole there and hit the wearer without much problems: rigid armor was quite bad at stopping bullets. If you make it ignore rigid armor (tyhat should be the top categories of armor in your universe) that should work. kilted/padded armor was still used since it offered some protection vs slashing and crushing damage, while being less cumbersome than steel plate and less noticeable as well.
The easiest way is to put a maximum to the ammount of protection armor can give you vs shooting. a +3 or +4 maximum soak should do the trick to make heavier armour a less dominant preposition.
Cheers,
Xavi
I think it worth mentioning that Blackpowder in the RAW would probably be a Philosophiae formulua a la A&A, and therefore, much rarer than in historical Europe, even if one can make a whole barrel per season.
Just want to chime in here. I have a love/hate thing going on with this part of the mythic paradigm. I really like real history, and I think making everything Aristotles said true in the setting, makes it too much fantasy, and really stops the setting in it's current era, so to speak. One of the books I would love to see in Ars Magica (but I guess Atlas would never make it) is one about alternate eras of play, perhaps old Rome, or maybe 14th century Venice maybe. But the mythic paradigm sets a stop to this.
Another think I don't like about the paradigm is the way the world is laid out. An explorer should be able to sail to the Americas, or even Australia for that matter. Magi, with their great power, should be able to be these explorers. But since these places doesn't exist in the setting (at least not as they do in our world) they can't.
But on the positive side, it really sets the setting apart and gives it a certain feel that is unique. I like that. 
That said, I have two ways of handling black powder in my campaign. The first is through alchemy, as in A&A and Sub Rosa. Nice article, by the way. But this kind of alchemy will not have the same effect on the setting as it had in real history. The solution is Maleficium. Enter The Lord of the Black Powder, a nasty demon who wants to see the world plunged into war and destruction. He starts a plot to teach men to easily create his black powder, which are basically charged Maleficium items. That bit was inspired by something I read, that many nobles saw gunpowder weaponry as "infernal" when it first appeared, "spouting flame and black smoke as Hell itself would". Nice. 
E.
I find this thread very helpful as I'm working on a New World setting (start 1580s) for Ars. Most of my work has been in what would the Order be like but this has given me new ideas for how to proceed with history at some points. Thanks to everyone for a great discussion.