I think getting rid of flat pen on items (maybe allowing certain champs to have some in their kit instead) would be a healthier way to go about it. Put all the Lethality stuff to % pen instead, and have them stack multiplicative instead of additive. Then Lethality runes could give you 15% pen, then LW gives 40%, so it's 51% total (just as an example). Exact values of items and runes would most likely need to be tweaked, but I'm talking mostly about the concept here rather than the numbers.
THIS creates a choice:
A) Build Lethality/Mpen to shred tanks
or
B) Build raw damage to shred squishies
Seems much simpler to design for, and easier for players to understand as well, while still creating an actual choice about who you are itemizing against.