PD does not have a defensive stat: it only has an effect when you hit the champ with it, which is something you most likely can't do against a LB or Syndra. Counter-arguing it with stating that Yasuo can hit whatever he wants with his Q and E would be an Ad Hominem fallacy. And why you say that it's good on Yas, but bad on everybody else? Didn't you make an argument about Tryndamere with PD?
Same with Muramana. Sure, it works with Ezreal, but what if I want to use it for lane Udyr cuz I don't like his manacosts? It's an option that others should be welcome to try.
Yes, there will be items that will not be good for anybody, and they may be removed from the game. But that doesn't mean that everybody should have their own personal core item. Or else it would lack diversity in League and become stale; and that would kill the one thing that makes players want to keep playing the game, which is the customization of items on certain champions. I'm pretty sure Guinsoo's doesn't just work with Kai'sa now. Varus, Kayle and Kog'maw (rest the voidsent's heart) can work with the new Guinsoo's. Sure Zephyr was deleted due to lack of use, and I can agree with that, but Sword of the Occult was a monster for those who could use it effectively, as it was stronger than Mejai's due to AD scaling for champs who only need that and nothing else like Zed, Riven and god forbid Rengar.
And for the record: Riot tried giving a core item to a champ once, named Viktor. On release, it never worked. So if we went with your logic on deleting items that are good with one champ only, should we delete Viktor's only way to deal damage through his mediocre un-upgraded items, and therefore delete Viktor's existence altogether? The answer is a resounding OH HELL NO! Riot buffed him, and made his hex-core completely viable, and people learned to build around it in the meantime.