Regarding what you said about Naruto, pretty much everyone is born with great potential, the prodigies being the ones who fulfill it at a young age, which doesn't exactly include Naruto.
Thank you for leaving out Jiraiya (he's just like Naruto), and you're also right about Konohamaru, Gaara, Obito, and Nagato. But don't forget we found out later it was Gaara's mom who made the sand move, not Shukaku
In regards to Kabuto, in terms of medical jutsu, he was definitely a prodigy. Shikamaru's kinda the same way, just in terms of intel and strategy rather than medical.
Sasuke, while I agree that's he a prodigy, you're kinda going about it the wrong way. Before the massacre even took place, he was said to be performing some of the clan's more powerful fire techniques, which is the real proof that he's a prodigy. His performance in the academy after receiving his Sharingan was basically driven by his desire to kill Itachi. His performance in the academy might've been different if that never happened, even if only slightly. Not hatin', just sayin' your data's a bit off.
The other prodigies you listed seem about right to me. Just don't forget Izuna. If he was Madara's equal, then he was likely a prodigy as well.