This gets me thinking about what the purpose of penetration is in the game, and what I came up with is this: I think penetration exists to help keep tanks from being to tanky, and squishies from being too squishy. Let's say I am a marksman, Malphite is on my team and building tank, and we're facing a Syndra. Now, Syndra gets Athene's, DFG, Z's hourglass, boots, deathcap. She's thinking about her 6th item.
Now, in pretty much all games right now, she's gonna get that voidstaff. And that helps me as a marksman. Why? Because she's building a lower AP item to help her deal with Malphite (and any other tanky ppl on my team). Without it, she can't even threaten him by herself. That's a bad enough situation for her that she's going to build voidstaff. With less AP, she can't burst me quite as easily; maybe I can get an MR item and actually survive her burst. Or at least force her to use all her abilities to burst me.
Without voidstaff, she just goes more AP, making it harder for me to survive, and making Malph harder to kill. I'm not sure that's good for the game. It becomes this weird mess of cat and mouse with their backline trying to kill our backline (and vice-versa) while just avoiding the tanks, since we can't kill them. I like the current system better, where the tank can actually be threatened, at a cost.
If there's no penetration, it seems to me like tanks become pretty much untouchable. I know it's a popular opinion that tanks/melee are useless right now and can't do anything, but damage dealers need an answer for tanks, ultimately. I'm not sure I can think of anything, besides penetration. We may have gone a little too far in this direction, but nobody wants to see league of bruisers make a comeback. That's not balanced either, and I'm not sure taking penetration out entirely is the answer.