I can't really...oh alright.
1. Shikamaru - completely me all over. And in the spirit of RakaMikazuki I'll go a bit long-winded. When we first see him, he's this kinda boring guy who doesn't wanna do anything, always complaining about what a drag things are. But then Ino jumps out to help Sakura and he's right there with her, dragging Choji. We first see his *ytical mind during the Chunin Exams, and then Naruto starts hanging with him more - and his match against Temari completely seals his fate as probably the best "Ninja" out of the Konoha Eleven(all the Leaf kids of the four teams minus Sasuke), considering he's tactical, weighs options, and knows when he can't win. He's aware of his shortcomings, and knows full well he can't Sixty-Four Palm people into submission or go on with tons of stamina like Naruto.
It's awesome that he becomes the first among them to become a Chunin, even though most everyone of the Eleven grew up so much from the Exams in their own way. Even more spectacular is watching Shikamaru progressively learn from every mistake and failing, becoming better and better to a point where he rarely complains something is too hard, or that it'll be a drag, because he has responsibilities and duties and he carries the Will of Fire. The best part is that he eventually becomes one of Kakashi's, then Naruto's, personal advisors. He shines just as bright as all the others, in his own unique way.
2. Hinata - In direct competition with Shikamaru for the spotlight, but sadly, I'm very much a Shikamaru so he's closest to my heart. Hinata, though, also is. Very shy girl, whole heapload of expectations, and her younger sister is stronger than her. Well...okay, that's relative, because she failed to beat down her sister when the time came to it because she was too compassionate, and lost the match. Overall, people have called her a better female protagonist than Sakura in this, but I think they're both good.
What I like the most about Hinata is that she grows...well. Probably the most out of anyone in the Konoha Eleven. She goes from a shy girl who can't do anything to a strong woman who would stand side-by-side with Naruto until she's physically unable to anymore. She's strong, intense, and though she's overshadowed, she's still a Hyuga, and proves it time and time again. She essentially spends the entire series becoming strong enough to make Naruto really notice her, and finally realize that she really REALLY likes him. Plus, they're a wonderful match! I watched the OVA for "The Day Naruto Became Hokage", and she's managing an entire family, plus responsibilities for Naruto and getting him ready. Being not just a warrior, but also a great mother, is something I c*so respect her for. Which brings me to...
3. Naruto Uzumaki. Yes, yes, I know, I know. I also like Gaara, Choji, Lee, and many others. But Naruto is here because not only is he the central character, but we also see him grow so much. Naruto has no real natural talent, no family to pass down techniques to him, and no real respect. So he becomes a prankster. I do like knowing that the Uzumaki bloodline is strong with stamina and fast healing, because that makes the entirety of pre-Shippuden much different. Healing from the stab wound to his hand before they meet Zabuza? Probably much more bloodline than Jinchuriki. Always recovering after a night of good sleep when learning the Rasengan? That went on for YEARS. Being a Jinchuriki just compliments his natural blood talents, which is probably the biggest genius of Minato's sealing. The fact that he had to think of it during one night of fighting a big ginormous ragebeast also proves that.
Despite what anyone says, I think Naruto's just as talented and smart as his dad. He learns the Multiple Shadow Clone Jutsu after just several hours of practice with a very good textbook - and later he learns he can apply Transformation to it for an infinite number of purposes, such as turning into a shuriken for Sasuke to throw, or the infamous Harem Jutsu, or even when he impersonates his entire team during the Chunin Exams. To be able to mimic them well enough to fool everyone is a testament that he actually does listen when it comes down to it, and observe. He's persistent, and takes inspiration from simple things, as we see with him learning the Rasengan. And he never wastes anything he's taught or that he observes, such as when he uses Kakashi's bum-poking Taijutsu and imbeds an explosive kunai right at the base of the Monster-Gaara's tail.
While his dad was faster than anyone who ever lived, Naruto is unpredictable. Much like when Kimimaro had to fight Drunken Fist Lee, you really don't know what's coming every time you fight Naruto, because you can only guess at what he's cooking up. He initiated one-half of a complex plan, correctly guessing that Sasuke would figure it out immediately and continue the second-half during the first encounter with Zabuza. He pulled sneaky simple tricks in the Chunin Exams like Transforming straight from Kiba to Akamaru to make Kiba freak out and punch out his own dog, or using a clone to hide the hole from him tunneling to pull off a Shoryuken maneuver on Neji. His genius is that he takes every small thing he learns, everything he sees from his friends, and figures out how he can apply it to make himself stronger.
Most importantly, though, Naruto knows loneliness, knows pain, knows abandonment, knows how hard it is to trust someone or earn trust, and comes out the better for it, and he can see exactly why. He's wise beyond his years for the rough childhood he had, and spreads his lessons to all the lives he touches. He appeals to Hinata, Neji, Kiba, Gaara, Tsunade, and just in pre-Shippuden! He never loses his love for being a prankster, or for being unconventional, but Naruto's not like other ninja. This is a good thing, because people start to follow him all over, his optimism spreading across nations and breaking the vicious cycles of hate and anger. At the true end of it all, though he can't teleport or do crazy seals or anything like that, and still relying on his natural instincts for strategy and using what he knows to its fullest, he takes on gods.
And then after things quiet down, his dream of becoming Hokage is fulfilled, but based on his attitude during the OVA, he's outgrown the need for it. He's earned it, and now it's a formality to have the ceremony. It's like settling in for your day job after going out and racing cars - he has to step back from playing ninja and oversee the entire village, and the fun part is, I think he's finally a person who can do that. As unfortunate as it is that his duties don't always allow for him to be home, he's basically any good dad whose job has long hours, and provides for his family. For a Hokage, the entire village is his family, though, and through all his interactions, I believe he's just as in-touch with each and every villager just as Hiruzen was, just as powerful as Minato was, just as caring for their health as Tsunade and with just as many hardships in his life as Kakashi. He's probably one of the best anime protagonists I've ever had the pleasure of watching.
...and I rambled. XD