Speculah:The War Between Good Guys Theory

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This theory suggests that both the witches and the magical girls believe themselves to be the "good guys." The conflict isn't good versus evil, but rather two groups of good guys fighting for their own methods of saving the world.

Witches Fighting for Revolution

The witches are former magical girls who believe that the world is inherently corrupt. They've realized that all use of magic will inevitably lead to the creation of evil forces. They're trying to recreate and purify the world in order to raise heaven from the ashes of Earth. They think that magical girls are only prolonging humanity's suffering in a flawed world.

Madoka will eventually be forced to choose a side. She must either defeat the witches and seal away the power that creates them, allowing humanity to stand on its own, or become the witches' leader and bring about the creation of a new world where everyone can be happy, but at the cost of destroying the existing world.

Kyuubey may actually be on the witches' side. He understands the dangers of magic and hates having to endlessly send magical girls to their deaths, but some spell or curse forces him to follow his assigned role and keep his mouth shut. He's trying to find a magical girl who will turn into a witch powerful enough to break the cycle.

This theory can be combined with The Global Reset Theory: Madoka chose to compromise by restarting the world the way it was, giving everyone a second chance, but with premonitions or subconscious memories in dreams to help them fix the mistakes and regrets of their previous lives. The show could be taking place in this recreated world.

Witches Trapped in Illusion

Another possibility is that witches perceive reality differently, through hallucinations or insanity, and think that they are the magical girls fighting against monsters, never realizing that those "monsters" are normal people and actual magical girls.

There has been speculation that the spinoff manga about Kazumi is actually featuring a witch. She lost her memories and wakes up to find herself in the form of a magical girl. It's possible that this is an illusion, and she's actually one of the witches the real magical girls will fight.