I wonder ever-so-slightly if this might be a part of the musical's subtle Jewish subtext.
Both Stephen Schwartz and Winnie Holzman are Jewish and much has already been written about the Jewish coding in the show. The themes of outcasts and systematic oppression, the Holocaust parallels in the plight of the Animals, and the fact that Elphaba has Jewish-coded physical traits, as do stereotypical witches in general: e.g. black hair, green skin that can be equated with olive skin, and in the case of Margaret Hamilton or Idina Menzel, a big curving nose.
The "false Chosen One" theme could also be equated with Jewish views about Jesus.
Not that I'm equating the Wizard with Jesus in any real sense, and I don't think Schwartz and Holzman meant to either! Every Jewish person I know, in my family and outside it, likes and respects Jesus the man and his teachings: they just don't think he was the Messiah. But too many Christian leaders across the centuries have been more like the Wizard, so an analogy can still be drawn.
Judaism and Christianity share the same belief in a Messiah, based on some of the same prophecies from the Hebrew Bible. But Christanity believes that Jesus was the Messiah, while Jews don't believe that Jesus met all the requirements to have been the Messiah, whom they believe has yet to come. And this "rejection of Jesus" is a main reason why Jews have been hated and persecuted.
Likewise, in Wicked, the Wizard is believed to be the savior foretold by an ancient prophecy, and the fact that olive green-skinned outcast Elphaba dares to say "No, he's not the one, he doesn't match what the prophecy said" (among other things) makes her Public Enemy #1.
Of course, the fact that Elphaba herself does fulfill the prophecy adds a whole other twist to the scenario. Looking at it from a Christian viewpoint instead of a Jewish one, Elphaba can be seen as almost a Jesus figure: the prophecied savior who finally appears, but isn't recognized, and is vilified and condemned for speaking out against corrupt authorities and in favor of outcasts.
Still, keeping in mind the musical's other Jewish-coded aspects, I think the creative, tragic use of the Chosen One archetype is worth looking at from a Jewish perspective.