I agree that flat pen should come out first, but they've had %bonus pen before, but changed it to %total pen, while also significantly lowering the actual percentage penetrated. I think the AD item used to be 40 or 45% bonus pen, and now it's 25% total pen?
It's probably better that it's %bonus pen, so that they're not getting extra damage against targets who don't build armor... I think void staff has always had %total pen, or at least for as long as I've paid any attention.
As it stands now, assassins can use the %total pen in combination with their scaling flat armor pen (lethality). Maybe it's a good thing for them, but, honestly, I don't think they should have an option that gives them kill pressure against tanks AND squishies at the same time. Their job is to kill squishies, an ADC's job is to kill tanks. Why there's an item that allows both classes to do both things is beyond me...
Still, 45% bonus penetration does negate about half of the gold you spent on armor, and with the change to tank items now offering more armor and less HP for the same gold, going back to bonus penetration wouldn't necessarily be the only adjustment needed for tanks to feel like tanks again. Having to build 2-3 items before you're remotely able to soak up magic AND physical damage is rough as it is... since tanks scale with CDR and fall off when ADCs are shredding them with armor pen and crit. Oh yeah, and don't forget the enormous amount of true damage and resistance penetration being added to champion kits lately. Thank god conq no longer has any true damage.
That's another thing, too, if tanks want to get a lot of CDR, they've gotta build MR items or armor items with minimal HP. This is very very dangerous into comps with multiple sources of true damage. (Most true damage seems to come from AD champs). Righteous glory is the only somewhat decent tank item in these situations, but it's not very good on off-tanks. Other armor items that offer a sizable amount of HP don't have any CDR.
So, frozen heart into AD champs with true damage and armor pen, like old conq yasuo, black cleaver top laners, fiora, vayne, yi... the list goes on. It just isn't effective. Also, %hp true damage and especially %max hp true damage are some of the most busted pieces of any champion's kit... The only defensive counter would be shields and healing, since they don't amp up %hp damage, and protect somewhat against true damage... But an item like Sterak's gives a shield scaling off of HP, so it's a give and take that you inevitably lose.
To be fair, champs with those damage types are tank busters, but why then are they so effective against off-tanks who are sometimes designed specifically to counter those champs? Like divers into Vayne. I'd rather them have armor pen instead of true damage, so they're more effective against tanks that itemize against them and shred them late game like they should, while also not being very effective against champs that stack HP/AD items. Although, possibly negating the need for an armor pen item could be catastrophic... So who knows...