The Third Hokage
The Fourth Raikage
Shikamaru and Neji are two of the main characters that could use more attention, but, the most obvious underrated character from Naruto is without a doubt.
Tenten. She has a lot to offer in fighting skills etc. Even though it's just weapon-based. But she can offer more then Kishimoto lets her do.
Juugo. Sure he loses everytime he's on screen, but he fights the strongest ninja in the manga when he does, so there's nothing wrong with that. He'd cut a swaith through most of the rookie 9.
Despite that, I'm actually going to go with Kakashi. Dude is probably the strongest ninja who isn't Kage-level, and he only has 1 hax technique that he can't even spam. Even though Itachi beat him with Tsukuyomi pretty easily, during the ninjutsu exchange, Kakashi was holding his own, even while protecting Kurenai. I think since Gai beat Kisame, he's not underrated anymore, lol, but Kakashi always seems to get bashed here. He uses all of the strengths of the Sharingan WITHOUT having Uchiha or Hashirama DNA, he awakened the Mangekyou Sharingan, he's got a wide variety of Earth, Lightning, and Water techniques, and if we're talking strategy and fighting like a "ninja" should, Kakashi is near the top of that list.
Neji. nuff said...
Prodigy with byakugan ( most strong clan and taijutsu in konoha in part1), then in shippuden a normal jounin...
A is the most underrated character imo. people think he can't stand kisame,itachi,pain ecc. but they forget he has got an amount of chakra comparable to a biju's,an that his speed is the best behind minato and naruto's,therefore he should be abe to blitz anyone if he wishes. but kishi made him too stupid,that he ended up losing his arm,and he didn't use his second version to defeat sasuke while he still could.
got won over by the Tsunade argument so.... i'll go for Tsunade-sama.
Hiruzen Sarutobi, he was and is still a badass, but never had the chance to show what his prime lokked. ^^
People really think she can't do anything despite her carrying the mantle of Hokage. When really she is probably the worlds best support type and a brutal close range fighter.
Going with Deidara. With his abilities he could nuke an entire village out of nowhere, just think about it. Had he just flown over Konoha and dropped a C3 the entire village would be gone, Pain style. His abilities were really used horribly by Kishi, he had such potential (not to mention as an Edo Tensei, think about what he could have done to the armies...). There's very few characters that can actually beat him as he's almost impossible to touch when he's already high up in the air.
I give this one to Suigetsu....he was powerful and interesting enough to capture Orochimaru's attention...he is basically immune to most jutsus out there, and he is regarded as a special kid even within the 7 swordsmen...yet he is still treated like fodder
Naruto. He has absolutely no skills and is as dumb as a post, but he is protected by plot armor and has infinite chakra whenever the plot calls for it.