Let's just start with some data
Enemy armor - 40 Our Armor pene - 9x1.28 + 3*2.56 = 19.2 We dont have any masteries (don't make this too compilcated) In the end enemy armor is 20.8 - this gives much more than 15 AD from runes as early armor scales very well
Look, early armor pen helps with trades while AD helps with farming. Although, farming gets better with practice but what is constant is the enemy champion. That AD you sacrifice in runes to get armor pen, you get far more in return with effective damage. Most champions have less than 20 base armor and with the armor in runes, their effective armor is about 5 at level one. Now, since you have masteries, you start with 25 armor pen at level one and chances are that your enemy will have less than that, thus, you do true damage for the first levels. After you get youmu's which usualy happens at lvl8-lvl9 you will have 48 armor pen and they will have about 40 armor. So, basicaly, you have enough armor pen to do true damage to them till level 11. So, by focusing in raw AD builds beyond that gives you a lot more effective damage. And i have actualy seen that in game many times and also in mirror matchups. Zed v Zed and i always did more damage with my Q while they had less armor pen in runes and they also had dft instead of td in masteries. It was one zed that admited that my Qs do twice as much damage as his legit and he had about 30 more AD. Having huge armor pen advantage over your target makes a huge difference since damage reduction from armor is exponential and not linear. Having 10 effective armor means a lot more effective damage than having 15 effective armor, yes, 5 armor makes a difference. In order for AD to be more affective than armor pen, you need a lot more of it. At level 9 with youmus and 48 total armor pen you have 160 AD and you do as much damage as if you had 250 because of the fact that they have little to no effective armor. It's like, i took away 95% of an Ahri's HP with just W-E-Q as Zed hitting both Qs and with thunderlord's that was about 120 damage. at level 10 and the only thing i had was a youmu's and a longsword. She was lvl9 and she had 45 armor while i had 49 armor pen. Even late game, on a squishy target, your burst is insane. Do not underestimate armor. With 531 ad at full build i do the damage that others do with almost 100 AD more on the same champion. The more the armor pen, the more damage you do in comparison to raw AD. Like, go full AD, get 500 bonus AD on zed and hit everything but having no armor pen and go then with 53 armor pen and 418 bonus AD and do the same and then calculate the reductions and compare the results. With a quick calculation on a target with 80 armor, with 
as the attacker, hitting 3 Qs, 1 E and 1 AA, with 500 bonus AD and with no armor pen, you get a total actual damage of 1479 and with 418 bonus AD and 53 Armor pen, hitting the same you get a total effective damage of 1883. That is the damage that they suffer, not the raw. You see? The difference more than considerable. In one case you did a good chunk while and wait for the mark to pop while on the other you might have actualy killed them and if they had a Qss they wouldn't have the time to use it... Armor pen has a big impact
Early AD helps with last hitting creeps in lane, which is a big factor in determining how trades play out. Early trades are more or less dictated by who has the superior farming position, and who can position aggressively relative to the wave and their opponent. Taking flat armour pen might be decent if you plan to hit the enemy champion and only the enemy champion, but it won't do you any favours when trying to accrue early gold from minions.
Early flat armour pen also doesn't scale as well as flat AD. There are a lot of AD ratios in the game, and if you're taking flat AD reds, you most likely have 2 or 3 of those scalings yourself. Nothing scales with armour pen, to my knowledge. Simply buying more armour will instantly defeat the effectiveness of flat ArPen reds. If someone buys more armour against your flat AD reds, you can buy more AD to boost your scaling abilities, or buy some ArPen (whether flat or %) of your own so that your existing AD will do more work for you.
Speaking of builds, it's better to get 15 AD from runes and build ArPen than it is to get 19.2 ArPen from runes and then sacrifice an ArPen item for an AD item (or vice versa).
why dont you get this?
AD runes is for the early game with shit scaling Armor pen is for champions that scale well into the late game.
Them going from 40 armor to 20 is only about a 1/7 increase in damage, whereas you going from 60 AD to 75 is like a 1/4 increase.
Thus the AD does way more than the armor pen at level 1. Everything just snowballs from there.
So AD is just way better. If you run armor pen, figure you'll be poked out of lane or zoned while you're still at like level 2 or something. Then they'll just get more gold and then they're stronger.
Ok so maybe I will introduce you what I just made in C# made by mixing every possible combination ps. brotip: I have found that Doran's shield is reducting your AD before any calculation will be made
Dunno if this is worthy post, but if you like it just upvote http://i.imgur.com/l6Yg2Wz.png
And yes, no matter how I will increase the armor value this runesetup won't change based on effectiveness
I used for that only runepage, no masteries included, and the formula for enemy damage reduction was 1-(100/(100+armor))
