You are ignoring several factors.
First off, no she hasn't, I am not talking about pro-play I am talking about the actual player base. You know the thing you and I are a part of.
Secondly, I acknowledged that Akali was played by "fools" which brings her winrate down, but this doesn't make her a bad champion, in fact, she is still arguably one of the strongest in the game. I don't worry about her, I play jungle and she's not really a big deal to me. Your argument, however, was that mages are too strong and Akali is an example of a meta pick strong against those OP mages. Just because you have to be good with her doesn't mean she isn't strong into almost all mages.
Your third point is laughable. You are saying it is okay for AD champions to get a large AP shield because without it they lose? Your arguments basis is that because the mage is ranged you need a shield to help against poke, weird I thought there was already one in the masteries, I must have been mistaken (I'm NOT). My argument against it is that one item seriously inhibits the kill potential of any AP damage while still adding more AD to that champion. You don't see people building Seeker's Armguard and suddenly able to survive a Zed combo, and you shouldn't see that the other way around either.
You are arguing nothing with your last point. You say that because mages can be outplayed but people don't pick the counter its an insta-loss. Any champion can outplay any champion, what are you on about? Garen literally can keep mages in check, runs at their low mobile asses and silences them, then spins to win and presses R, Garen can 1v1 several mages if he dodges one skill shot. You name several champions who are viable into mages (even though this is a shit example because there is only one "meta" top lane mage, Viktor the next closest thing isn't even in the top 25 most played champs at plat+); if someone picks Ivern, why would I not pick Warwick and invade them all day? Having counter picks does not make other picks useless, its less about who you play and more about how you play.
Mages having strong counter-picks is a good thing, but this doesn't mean other picks are useless, Viktor blows his load and Jax survives? Well, Viktor is now dead. If you could survive a mages combo like it were nothing then they would serve no purpose at all.