In a meta sense, the fact that the film is honest from the start about its artistic license to the original text.
While at the same time they tell you that they really did their research; interviewing dozens of religious scholars from three different faith groups in order to portray the events as best as possible.
Many, but the whale shark scene is one of the first that comes to mind.
From the very first scene, the camera pulls back to reveal the stone head of pharaoh being pulled by hundreds of animated Hebrews. At that moment, you know this is going to be an Epic Movie.
The plagues is one for God. For once, He lets loose with His full power. And there is not a thing the Egyptians can do to stop Him. The highest point would be the scene where God kills all of the firstborns of Egypt— including Rameses' own son, which is finally what breaks Rameses and causes him to free the Hebrews.
A little digging into Egyptian beliefs brings out a new level to this. God isn't just using generic plagues to attack the Egyptians. He is mocking the Egyptian gods in the process, who tended to be patterned after animals, as well as the concept of Pharaoh being a god himself since this entire time he is powerless. Essentially, he is breaking the Egyptians by saying "See how your gods tremble before me?" in addition to suffering.
Their gods don't just tremble; they flee. He has full authority and power, and the various Egyptian gods can't do a damn thing to stop Him. Here's a brief breakdown of how every single prodigy before the Exodus hit Egyptian beliefs and their very way of life:
the staff-to-cobra transformation caused such a panic because it's a symbol of two goddesses: Meretseger, the guardian of the royal tombs, and, most importantly, Wadjet, the symbol of the royal power of life and death (hence why the pharaohs and a few other members of the royal family wore a stylised cobra on their heads). That's also why Hotep and Huy could pull it: they are the court mages, playing with cobras is part of their job;
the Second Plague, the frogs overrunning Egypt, continues the mockery of a good omen: the frog is a symbol of fertility and the god Hapy, a personification of the flooding of the Nile and its fertile silt, and smaller 'invasions' of frogs would come right after the flooding;
the Third and Fourth Plagues, the mosquitoes and the fleas, are a direct consequence of the end of the Second: there were no frogs to eat them anymore. What's worse, the Egyptians were used to deal with them, but this time there were too much;
the Fifth Plague, the disease of the livestock, hits a soft point of the Egyptian believes: the cult of Apis, intermediary between men and gods, with a living incarnation as a bull (the Egyptians also built graves for these bulls). Because now Moses is the intermediary, Apis dies, and no other bull with the proper markings shall be found;
the Sixth Plague, the boils, hits particularly hard: boils and other illnesses fall under the dominion of Thoth, the God of Science and Knowledge, Medicine and, what's worse, the Arbitrator of the Gods, who would bring justice and properly administer the law. Between the epidemics and the priests having no knowledge on how to cure this, this one is a warning that Egypt has brought itself outside of the law of Maat, its greatest moral value;
the Seventh Plague, the storm of fire, is personal for the Pharaoh and the royal family: storms are the dominion of Seth. In this time not only Seth is not yet demonized (that would happen only from the Twenty-First dinasty, and the names of the Pharaohs indicate the Nineteenth), but it's one of the most important gods, with Rameses's own father being named after him and the current capital of Pi-Ramses (cited by name in the Bible as the starting point of the Exodus) is a center of Seth's worship. Ouch...;
the Eight Plague, the locusts, is pure nightmare: while in small numbers they were considered symbols of luck alongside grasshoppers, in large numbers they were rightly feared, and by being brought by the wind this plague entered the dominion of one of the most important gods, Amon;
the Ninth Plague the Darkness, is again personal with the Pharaoh and his family: not only the authority of the Pharaoh is associated with the Sun God Ra and the Sky God Horus, but the reigning Pharaoh is Rameses, meaning "Born from Ra". A message of paternal and divine rejection?;
the Tenth Plague is linked to a specific Egyptian myth, the Eye of Ra. In that myth, the men had disrespected Ra and planned to rebel and kill him, so he sent his Eye (identified with either the war goddess Sekhmet or the gentle HathorDepending on the Version) to punish them with a slaughter... And in one day she killed half of mankind, all the guilty and many innocents, and to stop her finishing the job the gods had to get her drunk. The message here is: "Let My people go, for if you continue to sin all of Egypt shall die in an heartbat". No wonder Rameses finally relented...
The entire burning bush scene, especially when God comforts Moses and says that he will smite Egypt with all My wonders. The music, the effects, everything about this scene gives me chills everytime.
And afterward when Moses runs back to Zipporah to tell her what happened. No dialog at all for a full 30 seconds, but the joy of one man telling of his experience of God is conveyed utterly and emotionally all in that wonderful music and the way Moses moves to tell the story of his new divine calling. That gives me the chills every time. Just Hans Zimmer's sweeping score and Moses telling what happened through gesture.
The parting of the Red Sea is a Moment Of Awesome for both Moses and the animation studio.
And just before it, the Pillar of Fire. Which has the audacity to make its appearance by erupting up from underwater. It's just kind of awesome that after throwing all those natural disasters at the Egyptians, God's response to them still coming after His people to show his wrath in the most dramatic way possible.
While it's pretty scary, the entire sequence of the first 9 plagues, along with the amazing musical number, featuring a Dark Reprise of the song "All I Ever Wanted," is nothing more than awesome, even if it is one of the scariest things God has done since leveling Sodom and Gomorrah. The song itself is great, especially the lyrics, such as "I sent my scourge! I sent my sword! Thus sayeth the Lord!" The 10th plague though...
Pretty much every musical number doubles as this.
The entire When You Believe piece. It starts out as a single voice, joined by another, then a small group, until finally the entire nation is singing praises to their God for liberating them from slavery.
The animation in this movie is flawless, not just in its appearance but in it's implementation, with every scene being framed perfectly. The direction of this movie is masterful.
Tzipporah openly biting the hand of a prince of Egypt! Why is this badass? Because she probably knew that doing so could get her beaten or killed, but she does anyway because she's a woman who won't take crap from anyone! Including a prince.
Then, how she was able to escape with no one detecting her (except Moses).