No real order to these but...
Neji: He mastered the Juuken before he was even a Chunin, and the wind palm thing was of his own creation right? If this is the case, he mastered his clans style and created a jutsu to make up for their weakness (long range opponents).
Itachi: Extremely gifted and highly intelligent. He planned his entire life, and even his death, out. He's been pulling strings and manipulating things his whole life, and even while in the grave...and as far as I know...he had no one give him anything, he worked for all his own power and was blessed with incredible intelligence.
Minato: Another extremely brilliant shinobi who wasn't given anything, but created several jutsu from scratch. He created a way to legitimately teleport using tags, and created one of the most overused, overpowered jutsu in the Naruto series...
Kimimaro: How has no one mentioned him? The only Kaguya we've seen and his skills were enough to push drunk Lee, who is strong enough to cause Guy to be serious to take him down, and Gaara to the limit...in which case he only lost because sickness killed him. Another naturally talented shinobi.
And since I'm getting lazy I'll just name the rest.
Kakashi
Shikamaru
and the little bit of Shino we've seen has shown he's an extremely talented shinobi.
I think this list of "prodigy" is being confused or misinterpreted as who's the most powerful. A prodigy is just a naturally gifted shinobi. Half of the characters that are getting mention have been gifted powers, whether it be Sasuke's eye techniques or Naruto's tailed beast powers.