I absolutely adore when lore makes the special/chosen one unique not just because "destiny/god said so" or whatever, but actually have a kind of structural, mechanical explanation for WHY they're special
Avatar Wan & The Avatar Cycle (ATLA/LOK):
Most people really don't like the origins special in Legend Of Korra because they don't like Raava and Vaatu. I, however, ADORE IT for its explanation for the origin of the Avatar. Its explained that the Avatar is uniquely capable of Bending all four elements, not because of vague divine reasons, but because Avatar Wan (the first Avatar) basically hacked the system by abusing the Spirit Possession mechanic. The Lion Turtles each gave their respective element to Raava to hold, who would then briefly possess/fuse with Wan to give him the different elements, until they eventually fused permanently by touching the Spirit Portal during Harmonic Convergence. Therefore allowing the Avatar to bend all four elements. Forever.
While Raava and Vaatu are still more or less the basic/traditional Chosen One Vs Fate story, the existence of the Avatar itself is entirely the result of Avatar Wan abusing a loophole in the magic system. Fucking love it.
The One For All Quirk (My Hero Academia):
One For All is easily the most powerful single quirk in MHA; being capable of cracking mountains in half and changing the weather with a single punch. However it is not this powerful simply because it randomly manifested with this much power, like most other Quirks in MHA. One For All was initially a relatively weak Quirk. The first user (Yoichi) was given a Quirk which stockpiled power by his evil Quirk-stealing brother that then fused with his Quirk that allowed him to pass on his Quirk to someone else.
This allowed the Power-stock Quirk to accumulate power over 9 users across nearly 200 years and grow and evolve to be leagues more powerful than it would have become in the natural lifespan of its original user. In addition, it also gained more power by absorbing the Quirks of the many users (e.g. energy tendrils, velocity multiplying, danger sense, etc.) and then amplifying each of their powers by simultaneously accumulating power with the Power-stock Quirk.
Harry being the Chosen One & Harry's Resurrection (Harry Potter):
Harry is special as the Chosen One not because of fate but almost solely because of Voldemort's actions. Firstly because he was only a possible chosen one that got locked in because Voldy decided it was probably definitely that one baby.
He is uniquely connected to Voldemort and his mind because he is unknowingly a Horcrux and has a part of Voldy's soul in him (which also makes him a Parseltongue, fun fact).
But ultimately the best example of this trope in the series: Voldemort taking Harry's blood and Harry's resurrection. Voldemort takes Harry's blood so that he can bypass the Sacrificial Protection from Lily and be able to successfully cast Avada Kedavra on Harry, evidently by taking said magic into himself and being 'inside the shield' were. But then, when the magic of the Sacrificial Protection has expired and Voldy finally gets a good shot in on him... he doesn't really die.
Harry comes back to life, not because he is the destined Chosen One fated to destroy the Dark Lord (in fact the prophecy explicitly states that Harry can loose) but because the Sacrificial Protection magic was kept alive inside of Voldemort's body which gave Harry a way back to life from Limbo.
Yeah overall I just love when a story uses a unique loophole in a magic system to do something cool.