Madara is a buffer/chakra battery, who works only with konoha ninja. He isn't immune to CCs and he is really squishy. being immune to pure tai is quite a bad attribute, since most of the most powerfull or common mysteries are pure nin (angel konan, edo deidara, edo hiruzen) or both (kurama naruto, roshi, edo hashirama).

Naruto instead is a great DPS, who can potentially (and will) spam his mystery every turn. He can dodge like masked and minato. Has a strong CC (immobile) on his chase and could chase himself (both auto and mystery). Also he can make another unit immune to debuffs for 4 rounds.

Madara is simply more flexible, can be used with a lot more teams and can give you more utility thanks to immobile. Madara is good, but he isn't at the same level as naruto.