Penetration isn't necessary. It's just a damage increase that gets worse as they buy defenses.
Just as an example, 15 magic pen vs base level 1 MR of 30 means instead of doing 76.9% damage you do 86.9% damage. That is a 13% increase. Ok that's pretty good, but it's not different from getting a 13% increase by some other means. The drawback is if the enemy buys MR that percentage drops.
So when I see some of the new runes with % damage increases I'm more excited about that than when I see penetration. Percent damage increases are always good. If you have 10% increased damage it doesn't matter if the target has a lot of defenses or a lot of health. Your damage relative to their EHP increases by the same amount either way.