User blog comment:YurdleTheTurtle/New AD/Armpen Setups for Season 3 - Quick Tips/@comment-5839977-20121208184010

I believe the reason Riot reduced Armor Penetration on runes was because of the change in how the ArPen applies. Before, the "Flat" ArPen applied frist, and percentual came after. Meaning Flat ArPen was effectively reduced percentually by you percentual ArPen. This meant that having those "24.94" Flat Penetration together with your lategame Last Whisper (40%) and ArPen Mastery (10%), for a total of 46% ArPen:

( 1 -  0,4 ) - (( 1 - 0,4 ) 0,1 )

This really meant you had around 13,4 flat penetration, as 46% of 24.94 wasn't accounted for.

Armor Penetration marks was still stronger lategame, of course, no doubt. But in season 3, the Armor Penetration system has changed. Now the percentual reduction is applied before the flat. This means you now get the full  19.2 out of your runeset. This is higher that 13,4. So in conclusion, ArPen has become even stronger lategame, though their earlygame has been nerfed.

[NOTE: The same system applies for Magic Penetration.]