I don't know if you guys are aware, but the latest patch on the test realm has a very significant change to the way ArPen/MagPen works.
Right now, there's reduction and flat pen. The patch changes everything so it's percentage and everyone is capped at 50% pen. But that's not where it stops. Rather then reduce the armor/MR amount by that percentage, it actually reduces the PERCENTAGE of reduction of the armor/MR. Let me illustrate the difference.
Old system:
100AR/MR = 100 / (100+100) = 50% reduction
250AR/MR = 250 / (100 + 250) = 71% reduction
So if you have a Last Whisper/Void Staff (both 40% reduction of their respective type) and then 10 pen runes, it'd go like this.
(100 * 0.6) - 10 = 50 effective AR/MR, or only 33% damage blocked (down from 50%)
(250 * 0.6) - 10 = 140 effective AR/MR, or 58% damage blocked (down from 71%)
Under the new system, this is actually what happens. I'm sure the pen runes will be reworked, but we'll assume they're maxed and we've hit the cap of 50% penetration.
100AR/MR = 50% reduction * 0.5 (pen) = 25% reduction (effectively 34 armor)
250AR/MR = 71% reduction * 0.5 (pen) = 35.5% reduction (effectively 55 armor)
So as you can see, the proposed changes punishes you for having more resistance and actually promotes that the DPS classes never get it. This will also gimp tanks like Rammus and Morde who depend on those resistances as opposed to Alistar or Shen who mainly tank through abilities. Supposedly, the change in the system is to address the specific concern of penetration being too powerful in the first few levels. To which I say, why not simply scale back penetration runes? I think armor ones are way overpowered anyway.
edit: Of course, this doesn't take into account that maybe Riot is a little smart and rework penetration stats so Last Whisper/Void Staff only gives 10-15% instead of 40%. But that might give them a little too much credit.