I believe the reason Riot reduced Armor Penetration on runes was because of the change in how ArPen applies. Before, the "Flat" ArPen applied first, and percent came after. Meaning Flat ArPen was effectively reduced percentagelly by your percent ArPen. This meant having those "24.94" Flat Penetration together with your late game Weapon Expertise (10%) for a total (46%) ArPen. This really meant you had around 13.4 flat penetration, as 46% of 24.94 wasn't accounted for.(40%) and
Armor Penetration marks were still stronger late game, of course, no doubt. But in Season 3, the Armor Penetration system has changed. Now the percent reduction is applied before the flat one. This means you now get the full 19.2 out of your rune set. This is higher that 13.4. So in conclusion, ArPen has become even stronger late game though its early game 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 percent penetration. In Season 2,rarely saw use since it didn't build into any stronger item and, once you got , the MrPen from was rendered almost useless, making little more than a big delay in your build's progress, for mediocre stats.