I think the penetration buff is one of the reason that AP champs are so hurt, they have an increased base MR and ARM to counter the fact that they're so squishy, this later falls off on SR when champs start buying pen. I think to counter the initial pen, tank runes like MR and Arm can really help AP champs, Malz is a beast and with the ease of itemization for AP and Mana regen champs don't need to focus on buffing their early game with runes, just saying. AP champions are even more squishy but with some MR, ARM runes you can get a little less squish