In terms of whose written the best I'd say it's probably the Uchiha brothers, Sasuke and Itachi, for the sole reason that they were clearly Kishimoto's favorites. Kakashi and Tsunade are pretty well written (suprisingly on Tsunade since Kishimoto tends to butcher his female characters).
My personal favorites are the three sannin.
Orochimaru is just about the only character in the manga who has no sense of morality, no sense of good and evil, no sense of right and wrong (the only other one being Kaguya and she had about as much personality as the Juubi). He thinks himself above such human fallacies and acts only to entertain himself. He creates war between nations because it's fun. He's got a major god complex without a sense of self-righteousness to **** it up (i.e. Madara, Nagato, Obito, etc.). And while it's hinted throughout the story that it was his exposure to war and death that made him this way it's also hinted that he's been a little twisted since the beginning. His vices are his greed and his arrogance. Combined with his extreme intelligence (probably the most intelligent character in the manga outside of battle) and sociopathic tendencies, and Kishimoto keeping his hands off of him in part 2 (because that's when his villains started going downhill) Orochimaru would have made a great big bad for this series if it had gone in a different direction.
Tsunade is the embodiment of strength in this manga (and not just hulk smashing strength). The people she held dearest to her ended up dead in war and her two dearest friends left her- Orochimaru for his own selfish lust for power and Jiraiya on a fruitless endeavor to bring Orochimaru back to the light. She took the only two reminders she had of her deceased loved ones, her necklace her lover's niece and turned her back on the shinobi way of life. However when the time came for her to rise to the occasion she overcame her hemophobia and cynicism of everything the village stood for and stepped up to become the Hokage. She took leadership of the village at its lowest--shattered from the aftermath of the death of the third hokage as well as left in ruins after Orochimaru's attack. She faced criticism and resistance from Hiruzen's old advisers and had Danzo undermining her at every turn.
I don't have much to say about Jiraiya as he's my least favorite of the Sannin.
As a whole my favorite thing about the Sannin is that they almost seem to be the most human of the characters in Naruto. All three of them faded from their youthful optimism and ambition to change the world into jaded and cynical adults, giving in to their vices (Jiraiya his lust, Tsunade her love of alcohol and gambling, Orochimaru his greed and lust for power, knowledge, and immortality). With good reason of course, they'd been through two wars and seen the deaths of countless peers and mentors.