I guarantee you, you're thinking of "Needless".
Very, VERY few episodes , about 20-40 episodes
Needless has 24 episodes.
Includes superpowers (a girl shapeshifting , a guy learning everybody else's abilities , etc).
From Wikipedia: "The Black Spot eventually becomes populated by outcasts, some of whom, as a result of the contamination, gain various powers called "fragments". Those in possession of such fragments come to be known as "Needless".
Protagonist is a guy that learns the abilities of his foes, there is one more guy with this power who is supposedly stronger but I think he loses in the end.
From Wikipedia, the main character is "Adam Blade": "Adam Blade is a destroyer priest who lives in the church in Sector 533. He has a metal collar engraved with the characters '079.AB.' affixed to his neck. He has inhuman strength and endurance as well as accelerated healing, plus a skeletal structure attached with a special metal called Orichalcum. It was revealed that he is a clone of the strongest Needless, 'The Second Christ'. His only flaw is his attraction to cute, young girls. His fragment 'Zero' allows him to learn the attacks of his enemies, after being hit by it or seeing it, also being able to combine other abilities learned as well. His special move is 'Death Verdict', the final pronouncement when taking an enemy's life."
Its about a destroyed city or a war is going on and they are living in some kind of church
From Wikipedia: "This anime is set in the year 2130 (the beginning date remains unclear), 50 years after World War III. The war has left a crater where Tokyo once stood, a place now filled with contaminated rubble."