I would personally vouch for Madara being the most versatile character:
~Kenjutsu: Prowess is above average.
~Genjutsu: Strongest Genjutsu in the verse.
~Intelligence: One of the smartest characters in the Verse.
~Ninjutsu: Some of the strongest Ninjutsu in the Verse.
~Taijutsu (Skill): Prowess is above average.
~Speed: One of the fastest characters in the Verse.
~Summonings: Had the strongest summonings in the Verse (Kurama and Gedo Mazu)
~Healing: Has the greatest Self Regeneration in the Verse.
~Strength: Prowess is above average.
~Durability: One of the most durable characters in the Verse (The most durable?)
~Stamina: Has some of the greatest Stamina in the Verse.
~Weapon(s): Has one of the most deadliest weapons in the Verse (Gunbai)
~Doujutsu: He has the greatest mastery of Doujutsu in the Verse.
~Senjutsu: Has shown some level of mastery of Senjutsu.
The bolded are the things he has Naruto beat in. His Doujutsu kinda makes up for the inferiority he has too Naruto in Ninjutsu. He has the greatest Self Regeneration in the manga while Naruto is the best Medic (By which I mean, healing of others), so I guess you can say they are kinda equal in that aspect. He is also equal with Naruto in Taijutsu skill (As displayed when his Limbo clones and Naruto's clones clashed, although in the end, the Limbo clones came out victorious).
He has all the Haxx you can possibly need all the Paths, Izanagi, Limbo, IT, Omnyoden and Susanoo as well as the strongest Kekkei Genkai (Mokuton).
Needless to say Naruto is still a very versatile character, I just don't see him as being more versatile then Madara though. Sasuke is also someone I find just as versatile as Naruto (Possibly even more), Hiruzen is another hounerable mention.