1.Rock Lee-Loved his fight against Gaara and everything surrounding it, his backstory, his hard work and determination and his goal of proving you can be a formidable and splendid ninja without being good at genjutsu or ninjutsu, solely with taijutsu. Shame he didn't do much in part 2 but he remains my top 1 because of his role in part 1. Also liked his courage to go through with the surgery even despite the risks.Overall an endearing and inspiring character. Even the drunken Lee vs Kimimaru fight was entertaining and a cool reference to the film.
2.Neji-Despite his talent, he had to work his way without many of the benefits of the main branch and (for part 1 anyway) really showed you can be exceptional regardless of background (of course he was part of the Hyuuga clan but in that context). Wasn't a fan of his irrelevance in part 2 or the conclusion to his plotline regarding free will vs destiny but atleast he was content with things.
3.Nagato-My favourite villain easily. Compelling character and it was nice to see him have the same influences as Naruto, namely Jiraiya, his beliefs and his book, while going down a completely different path. Threatening antagonist, from what he did to Jiraiya to him destroying the village and taking out Kakashi, he really showed why he was one of the last Akatsuki and the leader of the group. His rinnegan was really cool but I especially loved seeing Naruto tasked with not only defeating a powerful foe but proving his ideology and methods wrong.
4.Gaara-One of the characters I enjoyed all throughout the series. From him being isolated all his life and harbouring hatred due to it to him changing and growing to such an extent that he becomes Kazekage after encountering Naruto was great (for his development). Also liked his moments in the war regarding his father and the truth about his mother and uncle. It was really nice seeing him go from cold and resentful to a more wise, mature and capable person.
5.Kakashi-Great throughout though sometimes he wasn't always impressive. He was dependable for the most part and I loved his gaiden, in between the two parts, showing us his past and what shaped his beliefs regarding the rules and how people who break them are viewed.
6.Might Guy-The guy had plenty of great moments throughout the series and was a really uplifting and caring master. From him stepping into the Lee vs Gaara fight to him supporting Lee in the surgery, he was great. He was the highlight of the last 200 chapters for me with his backstory and unleashing the 8th gate on Madara. Loved that the dude got to go all out and show off against the arc villain that had been hyped for hundreds of chapters. Overall, Guy was fantastic, in my opinion, and one of the characters I have few complaints about.
7.Obito-Really liked him in the Kakashi gaiden, with him feeling inferior and insecure about Kakashi but growing past that as he learns more about him and their bond grows. His disillusionment with reality following Rin's death at Kakashi's hands and Madara's influence was interesting to see and he made for a pretty engaging villain. Even as simply Tobi, the guy was fun to read.
8.Sakura-I had some issues with her in part 1 (though even there, she made an effort to grow and mature) and some parts of part 2 but she really proved herself in the Sasori fight (from her physical strength and skills to her medical prowess) and grew quite a lot since her early days. Her fight against Sasori remains one of my favourites in the series.
9.Sasori-Pretty sympathetic (though not to a crazy extent) villain with some cool abilities. Having his parents killed by the White Fang and only having their puppets to remember them by was pretty touching and him discarding the puppets and turning himself into was interesting. I liked him quite a bit and his fight is one of the more memorable ones for me in part 2.
10.Naruto-He might come off as pretentious at times but I still have a soft spot for his idealism and optimism as well as his disdain for the outdated and cruel things he sees in the ninja world.
Hashirama was pretty cool too.