"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 Weapon Expertise (Deprecated template: use Mi1 to Mi6.) (10%), for a total of 46% ArPen:(40%) and
( 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.]"
All in all, I believe flat penetration will see more gameplay than before, as it has become quite strong now. It's almost like just adding true damage, completely ignoring armor, and not decaying with precentual Penetration. In season 2, rarely saw use since it didn't build into any stronger item, and once you got the the MrPen from was rendered almost useless, making little more than a big delay in your build's progress, for mediocre stats.