I mean without kekkei genkai,tailed beasts,dojutsus just pure skill.
I vote Minato
I agree, Jiraiya said they haven't had a genius like Minato since Minato even though ninjas like Itachi, Shisui, Sasuke, Naruto, Kakashi, Neji, Gai, Shikamaru, and Lee all became strong/smart ninjas after Minato died. Minato was only 24 yet he fought 2 Kage level opponents (1 being a perfect Jinchuuriki) on more than 1 occasion and even caused Bee to tremble at the thought of him. He is the fastest Shunshin user without any ninjutsus enhancement like lightning armor, he is fast enough to even react to A's fastest attack at point blank range. Madara said Tobirama was held as the fastest of his time (makes him faster than Hashirama and Madara) and Tobirama said Minato's Shunshin was better than his own.
Minato eyes are pretty much on the Sharingan analyzing level, he can break down a jutsu by seeing it once and further break it down upon further observation. He's the only person to deduce Obito's Kamui alone and within seconds of seeing it while it took Kakashi with the Sharingan, the help of 3 other skilled ninjas to deduce how to fight Obito and that's in their second meeting. I believe had Minato lived up to Gaiden then he would be the strongest and most skilled ninja Konoha ever had (had he lived, I don't see Naruto and Sasuke getting Hagoromo powerup). Minato would be 53 now which is the age of the Sannins at the first part of Shippuden, yet all 3 were still powerful Kage level ninjas.