I think all chosen-ones face the accusation of being Mary Sues because it's inherently contrived.
If you want to talk about skillz, though, think about how this was handled in The Last Starfighter. Alex Rogan wasn't so much as chosen as he was awarded chosen-one status because of his high score on the game. He woodshed on it until he beat it. Meritocracy.
Or what about Willy Wonka? You see the other kids try to sort of game the system for their golden tickets. Charlie just got lucky. Yes, it's providence, but that and his ultimate gift of the factory is an award for goodness of heart.
Compare that to, for instance, Kirk's fast-track to command in Trek 2009. Cheats on his tests. Displays arrogance and chauvanism. And yet is told that he's destined for greatness anyway and the plot sort of hands command to him on a silver platter. Mary Sue.
And it's no coincidence that The Force Awakens, another JJ vehicle, suffers from this entitlement effect.
Rey isn't as much of an a-hole as Kirk, but she does not woodshed. She is given mad-skillz(tm) out of the ether.
It's always hard to root for a character who gets handed things on a silver platter rather than having to work for it and suffer various setbacks.
There are examples of female heroes who woodshed. Mulan, for instance, or Beatrix Kiddo. They're simply more compelling than Rey.
This is what life is
really like. You have to invest your 10,000 hours ala Malcolm Gladwell. Anything less than this is a junkfood fantasy.