Pain is a far more relateable character in that he wanted to protect those close to him but could not do so. As a result, he became bitter and turned against the world, believing that the only way to repair the world is to make it suffer. He mirrors Naruto in many ways, as they both trained under the same master and both share the same goal: to finally stop the shinobi world from constantly fighting. The only difference is their faith in mankind, and that is ultimately what turns them against each other. Their similarities make it all the more dramatic when they finally clash, as it feels like two idealogies dueling over what is ultimately right for the world.
Madara, on the other hand, possesses none of these traits. He has little in common with Naruto in terms of beliefs and as such the divide between them is too great for them to reflect each other the way Naruto does with Pain. A villain should embody a hero's greatest fear or flaw, and Madara fails to do that.