The answer to lethality woes is actually critial chance and onhit reduction + stronger mages

%critical chance and damage reduction and things to stop heal and effects.

Imagine

super cloak - passive 50 magic resist, 10% cooldown reduction, champions cannot critically strike you. critical strikes are not critical strikes but instead normal strikes with any other benefits they would have had if they critically struck. Lifesteal is still calculated based off damage dealt and stuff. Thornmail is calculated before damage reduction. Onhit damage is reduced by 25%.

active - dash in front of target ally and change the target of tower agro, you cannot use abilities for 1 second after the dash

With items like this around penetration will become a major damage source, let it happen. Its all that other stuff you need to worry about. Penetration is actually the healthy one.

In addition to this give mages more silly AP items with an aoe damage nuke in mind like but for dealing tons of damage using combos.

For example

Mage gem - 50 ap and some magic resist - make a big circle somewhere, enemies inside are slowed by 25%, lose 25% attack speed, and take 1% max hp as damage per second, you gain 50% AP while you are close enough to the center. Lasts 10 seconds or until you die. 300 second cooldown.

I forgot to mention, why don't mages in this game have anti attack abilities? I mean sure there's stuns but that power budget cost... Why is nasus of all champs the one with a magical suppression ability.