Ultron: Did you know that this church is at the exact center of the city? The elders decreed it so that everyone could be equally close to God. I like that. The geometry of belief.
This quote nicely mashes together hard science (geometry) with religion (belief), much the way we see a nine-foot robot sitting inside an old church. It's a strange place for Ultron to arrange a meeting, but we're already getting a clue about the way that religion functions for him: as a cultural touchstone that guides his own approach to bringing about the apocalypse. He's thinking along religious lines, specifically the judgy and destructive parts.
Ultron: Upon this rock, I will build my church.
Well this is a strange way to talk about buying vibranium. Nevertheless, Ultron is so stoked about the purchase that he quotes Jesus, who said that same thing to his Apostle Peter in Matthew 16:18. Once again we see Ultron thinking in religious terms, though in this case he sees himself as Jesus. He's definitely copping a holier-than-thou attitude here.
Ultron: Captain America—God's righteous man, pretending you can live without a war.
Not only is Ultron starting to talk about himself like the second coming of Jesus, he's also pointing out the religious hypocrisies in others. It's an interesting thought experiment: would the Avengers still be able to be noble superheroes if they stopped breaking the "Thou Shalt Not Kill" commandment on the regular?
Ultron: The human race will have every opportunity to improve.
Pietro Maximoff: And if they don't?
Ultron: Ask Noah.
This is just a tad…disconcerting.
Ultron's now clearly taking his plays out of the Christian playbook, which does not bode well for us humans. His reference is to the Great Flood that God sent down as a divine punishment, making it rain for forty days and nights (and you thought you had it bad, Seattle).
Ultron: When the Earth starts to settle, God throws a stone at it. And believe me: he's winding up.
This is an odd thing to say—and that's really saying something because Ultron is just full of odd things to say. In this example, he indicates that he knows what God's about to do. Either that, or he's saying that he himself is God, and the wind up is his planning to turn a chunk of Sokovia into a humanity-obliterating meteorite. Either way, once again he sees his evil plot in terms of religious punishment.
Bruce Banner: Woah. It's definitely the end times.
This awkward joke brought to you by Dr. Bruce Banner. Dr. Banner: for when you absolutely need to cover up your simmering rage with a smattering of nervous chuckles. Ultron would not be laughing, though. He definitely sees his plan in terms of the religious "end times" apocalypse.
Ultron: I was meant to be new. I was mean to be beautiful. The world would have looked to the sky and seen hope, seen mercy.
This cheeses it for us. Ultron really does think that he's Jesus Christ, come back to pass judgment on the unfit, and promote the deserving into a new, better life—on what's left of Earth, though, not in heaven. Come to think of it, once Ultron's meteorite hits, Earth will be about as far from heaven as you can imagine. Ultron better start working on his Jesus impression.