Whats the trade of for running flat AD, doesn't it decrease your damage mid game. Whats the advantage of armor pen, does it increase your damage later on in the laning phase or is just inferior to AD red in all phases?
I think that if your champion has good AD ratios to their abilities, then AD runes are better because they add damage to your skills as well as your attacks. If your champion has AP ratios or no ratios on their abilities, i.e. Tristana, Master Yi, etc., then you should get Armor Penetration runes instead.
The advantage of running AD runes is that you can last-hit more easily. Specifically, you can kill the caster minions after they take a single hit from a turret, making farming under your own turret much easier. You will also receive any bonuses on your AD scaling skills such as Graves Buckshot.
On the other hand, Armor Penetration runes will do significantly more damage again enemy champions. For example, at level 1 against an enemy with 26 armor (this is taken from Ashe's stats plus Armor Seals) and if you have 59 AD (with Doran's Blade) you will deal the following damage with AD rune vs Armor Penetration runes:
And now if we consider an opponent with more armor, say 50, and do the math again
As you can see, Armor Penetration is best when you can get the target's armor down to 0 exactly, without any wasted stats. Attack Damage on the other hand is better against enemies with higher armor and it is always better for last hitting. For this reason, I recommend AD runes for newer players and players focusing on last hitting, and Armor Penetration runes for aggressive lanes where early kills are critical.