Shooting into melee is not a good idea.  I don't think it's ever really supposed to be "safe" to do so.  With respect to your specific issue, I suppose a better shooter could actually be overconfident about his skills, and thus more likely to take a risky shot and hit a friend.  Also, a poor shooter is more likely to take wild shots that don't hit anybody at all.  So I really have no problem with the rule as it stands.  It's really supposed to punish the stupidity of shooting into a melee, regardless of shooter skill.  Sword-and-sorcery violence is supposed to be a bit more "realistic" (a better word might be "naturalistic") than the kind of antics we see from the likes of Legolas.  All that being said, if you ultimately don't like the rule, change it however you like.  (Here's a suggestion: an ally is only targeted if the original shot misses by 6 or more.  That would take shooter skill into account.)

In any case, it's always hilarious when PCs accidentally shoot each other.  Good times.

There's nothing wrong with hitting an ally. It's a good rule and should be part of the game.
But I think it doesn't make sense that the best archers are the most likely to injure the friends, while the worst archers have to be much less concerned about it.

FA represents a characters ability to get the weapon to hit where he wants it. And when you miss your target, you don't want the arrow to hit your ally. You don't aim at the gaps in your allies armor, it's pure bad luck if it happens.

Maybe a better solution would be to still make it an attack roll, but one that does not include the attackers FA and Dexterity. It's just 1d20 plus any magic enchantments, since the weapon does not know when to get through armor or bounce off.
Same chance to hit your allies for everyone, regardless of level.

Actually, the better your FA, the less likley it is that you are going to target your ally. You see the operative words made bold are, "if the attack roll is a natural 1-3, and this result qualifies as a miss..." So if your nat 3 is a hit, it is still a hit. I enforce the rule on any results of nat 1, though, because to me a 1 is always a miss.

Chainsaw wrote:

I think it makes sense. The best archers are more skilled, so if you happen to get in their way (1-3 on a 20, same as for anyone), you have a better chance of being injured (their attack ability is higher).

I don't see how that follows.

Starting from the situation where it's a given that the archer has rolled a miss and you are unfortunate enough to be standing in the path of an arrow that was meant for someone else, I don't see how the archer's aim would affect the chances of that arrow hitting you.  He wasn't aiming at you in the first place, so he clearly wouldn't have been aiming for areas exposed by your armor, compensating for your movement, etc.

It seems to me that whether you take damage or not should be completely random in this situation, so I agree with the earlier suggestion of making the to-hit roll against accidental targets using only any bonuses for equipment used, omitting the firer's stat modifiers and level-based FA.

Now that I completely understand the author's intentions (and the rules ), I think I can roll with it.

For other D&D-esque games we used a simpler (but more risky) solution: odd rolls are considered friendly fire when firing into melee. Much more risky, I must say, but it also eliminated another attack roll