I think I would divide the characters in 3 different sections first in order to know who's the most talented, in the end.
First, we have the players that were born with an amazing physique, the top athletes, and without a doubt Akutsu is the number 1 in this aspect, followed by Kintarou. He was born tall and strong, yet still remains fast and agile, so he could basically play any sport he'd like. However, I don't think he is as technically gifted as other characters, and I'm pretty sure he trained for months before the camp so his current skill didn't come out of nowhere.
Secondly, we have the players that are just naturals at tennis. I'd say the best in this category is actually Jirou (to the point that Atobe used to let him miss practices and still remained Hyotei's arguably second best player) but he didn't show any results in the camp (where he finally started training) that would justify this pick. The "tensais" (Fuji, Yuushi... Marui? etc) or even Ryoma, Kintarou, Niou and Yuki might have a better shot at this, but I'd be surprised if they didn't work hard to get where they are. I think Yukimura is probably the highlight of that group, skipping tennis for months and still remaining the beast that he is, the top player in Japan's MS tennis. Without those in mind, imo, the player leading this category is actually Mouri, who remained a regular at Rikkai without ever training (without being born with an amazing body like Akutsu's), and nowadays is the only 1st year HSer to be part of Japan's G-10. I'd give Kirihara a chance in this category for naturally learning the one foot split step on his own, without knowing it was even a technique, but that is basically all that is credited to him (to the point that speed is what made him a regular at Rikkai).
Last, we have the players that learn the fastest, which is a talent on its own. Of course, both Super Rookies are on top on this category with their incredible growth rates, followed by Atobe (who was the one that improved the most at the camp without actually training more, IIRC?). Kabaji would be the king of this category if he actually learned his moves instead of just copying them.
TL;DR, with all those in mind, the one character that keeps appearing in all those lists is... Kintarou, so I'd say he's the most talented player in the series. Internationally, the Dorgias Bros, Henri and Amadeus deserve a mention.