Most skilled?
1. Sasuke/Naruto: Consider the things that were being said about them near the end. Sasuke wielded chakra, as noted by the Kyuubi, on par with the Sage of Six Paths. Naruto created several clones, changed the shape of the Rasengan into several Rasenshuriken, and infused each separate one with the nature chakra of the tailed beasts. The Fourth Hokage, a genius shinobi, was unable to infuse his nature chakra or change the Rasengan's shape before his early death; Naruto did it with several at once.
2. Hashirama/Madara: Madara dueled and defeated the current five kage with nearly no difficulty; Hashirama dueled and defeated Madara AND the Kyuubi simultaneously. Seriously, modern day shinobi watched these two combat each other and were left breathless, never having seen such ninjutsu mastery before.
3. Itachi/Minato: It's hard to determine which of these shinobi is smarter, but the facts stand: they are likely the two most gifted and prodigious shinobi that are NOT carriers of the Asura/Indra chakra. Itachi, to my knowledge, has never lost a battle... exempting the Sasuke fight, a fight he willfully lost. Minato mastered Space-Time, created one of the most versatile offensive jutsus ever, and fought and killed one-thousand shinobi alone. Even the Sannin admit their inferiority to these two.
4. Orochimaru/Jiraiya/Tsuande: Though in different areas, generally these three are accepted to be somewhat similar in skill. Tsunade is a masterclass healer; Orochimaru is an elite pusher of ninjutsu limits, a genius in a time of war; Jiraiya is a freaking Sage, and nearly killed Nagato and his Six Paths (a shinobi who, at the time, was undefeated) without any prior knowledge of how the Rinnegan even worked... talk about impressive.
5. Kakashi: Climbed through the ranks with ludicrous speed, mastered taijutsu, genjutsu, and ninjutsu; advanced himself in a foreign dojutsu well enough to land a blow on a goddess; considered by Might Gai to be the highest authority on analyzing jutsus. Seemingly a match for any opponent, and the Sixth Hokage of the Hidden Leaf.