GrandmasterD hasn't done the math yet and I'm an impatient ****abish, so I'll do the math for him. For the sake of simplifying things, only marks will be considered. 9x Greater Mark of Armor Penetration gives 1.28 * 9 = 11.52 armor penetration

Recall that:
  • Damage multiplier = 100 / (100 + Armor - Armor Penetration)
  • Therefore, raw damage needed to deal 100 physical damage to the target = 100 / (Damage multiplier) = 100 + Armor - Armor Penetration

The lowest possible base armor in the game belongs to Sona at 9.3 armor at level 1. For the sake of making Armor Penetration runes be utilized at maximum effectiveness, we'll assume a hypothetical target which has exactly 11.52 armor. The math is as follows:

With armor penetration:
  • Damage multiplier = 100 / (100 + 11.52 - 11.52) = 1.0000
  • Raw damage needed to deal 100 physical damage to the target = 100 + 11.52 - 11.52 = 100.00
  • Therefore, 100 raw damage = 100 damage dealt, meaning you are dealing the equivalent of true damage.

Without armor penetration:
  • Damage multiplier = 100 / (100 + 11.52) = 0.8967
  • Raw damage needed to deal 100 physical damage to the target = 100 + 11.52 = 111.52
  • 111.52 raw damage = 100 damage dealt. You need a 11.52% increase in raw damage to compensate for the lack of armor penetration.

Since 9x Greater Mark of Attack Damage gives 0.95 * 9 = 8.55 AD, if the AD scaling increases your damage by at least 11.52%, then AD marks > Armor Penetration marks.

Now, remember that this is the optimal case scenario where Armor Penetration marks are the most effective (on a low armor target). Let's take a real-world scenario: Darius at level 1 has 23.5 base armor. Add in 9x Greater Seal of Armor = 12.69 bonus armor and Cloth Armor = 15 bonus armor, plus 3x Hardiness = 5 bonus armor and this comes out to a total of 56.19 armor. Let's do the math again:

With armor penetration:
  • Raw damage needed to deal 100 physical damage to the target = 100 + 56.19 - 11.52 = 144.67

Without armor penetration:
  • Raw damage needed to deal 100 physical damage to the target = 100 + 56.19 = 156.19
  • (156.19 - 144.67) / (144.67) = 0.07962. You need a 7.962% increase in raw damage to compensate for the lack of armor penetration.

Notice how this percentage is smaller than when the target had less armor? Now, I don't know about you, but last time I checked, 8.55 AD gave me a lot more than a 7.962% boost. Take Riven's level 1 BnB on a an average low-armor solo top laner who would prefer doing 21/9/0 instead of 9/21/0, Kha'Zix, with flat armor yellows and 3 points in Hardiness (18 + 12.69 + 5 = 35.69):


With AD quints, ArPen reds, and Elixir of Fortitude as well as 21/9/0 masteries:
  • Base AD = 56.75
  • Bonus AD = 2.25 * 3 + 15 + 0.67 + 3 = 25.42
  • Total AD = 56.75 + 25.42 = 82.17
  • Armor penetration = 8% + 11.52 + 5 = 8% + 16.52
  • Damage multiplier = 100 / (100 + (35.69 * (1 - 0.08) - 16.52) = 0.8597
  • Raw combo damage = 82.17 + (30 + 0.7 * 25.42) + (82.17 * 1.2) + (30 + 0.7 * 25.42) + (82.17 * 1.2) + (30 + 0.7 * 25.42) + (82.17 * 1.2) = 521.364
  • Actual damage = 521.364 * 0.8597 = 448.22

With AD quints, AD reds, Elixir of Fortitude, as well as 21/9/0 masteries:
  • Base AD = 56.75
  • Bonus AD = 0.95 * 9 + 2.25 * 3 + 15 + 0.67 + 3 = 33.97
  • Total AD = 56.75 + 33.97 = 90.72
  • Armor penetration = 8% + 11.52 + 5 = 8% + 5
  • Damage multiplier = 100 / (100 + (35.69 * (1 - 0.08) - 5) = 0.7822
  • Raw combo damage = 90.72 + (30 + 0.7 * 33.97) + (90.72 * 1.2) + (30 + 0.7 * 33.97) + (90.72 * 1.2) + (30 + 0.7 * 33.97) + (90.72 * 1.2) = 578.649
  • Actual damage = 578.649 * 0.7822 = 452.62

As you can see, even given optimal conditions (opponent did not run a full armor page or buy Cloth Armor, additional bonus AD which synergizes with armor penetration maximized with Elixir of Fortitude), usage of Armor Penetration runes still causes you to deal less damage. In a more conservative scenario where you don't have the elixir (which you won't after the nerf goes through):

With AD quints, ArPen reds, as well as 21/9/0 masteries:
  • Base AD = 56.75
  • Bonus AD = 2.25 * 3 + 0.67 + 3 = 10.42
  • Total AD = 56.75 + 10.42 = 67.17
  • Raw combo damage = 67.17 + (30 + 0.7 * 10.42) + (67.17 * 1.2) + (30 + 0.7 * 10.42) + (67.17 * 1.2) + (30 + 0.7 * 10.42) + (67.17 * 1.2) = 420.864
  • Actual damage = 420.864 * 0.8597 = 361.82

With AD quints, AD reds, as well as 21/9/0 masteries:
  • Base AD = 56.75
  • Bonus AD = 0.95 * 9 + 2.25 * 3 + 15 + 0.67 + 3 = 18.97
  • Total AD = 56.75 + 18.97 = 75.72
  • Armor penetration = 8% + 11.52 + 5 = 8% + 5
  • Damage multiplier = 100 / (100 + (35.69 * (1 - 0.08) - 5) = 0.7822
  • Raw combo damage = 75.72 + (30 + 0.7 * 18.97) + (75.72 * 1.2) + (30 + 0.7 * 18.97) + (75.72 * 1.2) + (30 + 0.7 * 18.97) + (75.72 * 1.2) = 478.15
  • Actual damage = 478.15 * 0.7822 = 374.01

As you can see, the gap widens. If the opponent bought armor, ran a more defensive runepage or mastery page, or had higher base armor like Garen, it only gets worse.

tl;dr: Armor Pen runes on Riven are dumb, makes you lose farm by making last-hitting harder, and doesn't even make you do more damage to champions even in the best case scenario.