It wasn't John specifically, it was that someone like John would emerge. The alterations she made are in everyone, though they show themselves in different ways (if at all) and often need to be turned on. Such as the memories of pre-devolution humans from the war that were put into humanity by the Librarian, so that personalities from that time can be awakened and recovered.
Yeah, I guess, but, I dunno, it was the same way with squibs in Harry Potter. I just think, J.K. Rowling, you bothered to make an awesome universe with magic and whatnot, and then you create a rule where a few just simply cannot use magic, no matter how hard they try? That's sucky if you ask me. I wouldn't want to be a squib in the Harry Potter world. I dunno.
true, but even those with disabilities can succeed in our world, Bethany Hamilton anyone? just off the top of my head, there are many stories about those with disabilities who succeed at amazing things, that one guy who can play the guitar with his feet cause he has no arms... dunno, just thinking aloud.
It's also the system (outside of Hogwarts) that existed before Voldemort's defeat. The system that let known Death Eaters reach the highest echelons of society, that Let Lucius Malfoy keep the Minister for Magic at his beck and call.