In canon, Lelouch ordering the retreat from Narita was because the Guren had its Radiant Wave Surger damaged by Suzaku, which his whole battle plan depended on. As this essentially abandoned the Japan Liberation Front to be destroyed by Cornelia's forces, this strained the Black Knights' trust in him. Here, the retreat is due to the Decepticons showing up and completely turning the tide of the battle. The rest of the Black Knights obey mostly without hesitation because they are getting slaughtered by the Decepticons.
In the Prime episode Partners, Arcee letting Starscream escape was a case of Revenge Before Reason, as she wanted to kill him to avenge Cliffjumper and ended up underestimating him. Here, this point is not present, as Cliffjumper is still alive. Rather, his escape is a result of Starscream managing to appear pathetic enough that Arcee and Kallen let their guard down and let him get too close to them.
In the Prime episode Stronger, Faster, a Synthetic Energon-enhanced Ratchet really lets Optimus have it—blaming him for the Autobots "squandering their resources," what happened to Cliffjumper, and not being proactive enough against the Decepticons, triggering Arcee's Berserk Button. Due to Cliffjumper being alive in this story, he triggers Kallen and Lelouch's instead of when he brings up Naoto's death and insults Lelouch after he reflexively activates his Geass.
In Tohdoh the Miracle Worker, Lelouch ordered the Black Knights to retreat from battle after finding out Suzaku was the pilot of the Lancelot due to shock at having to fight his best friend. Since Lelouch pretty much knew this from the get-go in Code Prime, he instead calls the retreat because Britannia has sent a massive group of Knightmares to reinforce the prison.
Kallen and Suzaku's conversation on Kamine Island was, in canon, a case of Both Sides Have a Point, with Suzaku noting the Zero's actions have resulted in many unneeded deaths, while Kallen rebukes him by asking what purpose her brother's death would have served. Here, due to the Black Knights undergoing Adaptational Heroism due to their alliance with the Autobots, while Britannia undergoes Adaptational Villainy from working with the Decepticons, the conversation is firmly a "The Reason You Suck" Speech toward Suzaku, who struggles to find a way to rebut her statements.
The SAZ Massacre. In canon, it was caused by Lelouch accidentally Geassing Euphemia. Here, it's caused intentionally by Megatron having her kidnapped and replaced with a Pretender.
In canon, Ashford Academy was seized by the Black Knights as a headquarters during the Black Rebellion so Lelouch could protect Nunnally while claiming to the Black Knights that it was of strategic importance. Due to Lelouch moving Nunnally to the Ark, which is the base for the Autobot/Black Knight alliance, Ashford is instead seized by the Insecticons, who take Milly, Rivalz, and Nina (along with Arthur) hostage under Megatron's orders.
Nina's Roaring Rampage of Revenge is different here. While the reason for it is for Euphemia like in canon, as opposed to Nina wishing to avenge Euphemia's death at Zero's hands, she wants to save Euphie from the Decepticons after learning of her abduction.
The Black Rebellion still ends in failure and defeat for the Autobots and Black Knights, but unlike the canonical failure which was caused by Zero abandoning the Black Knights to rescue Nunnally on Kamine Island, the cause of failure is brought about due to the Decepticons launching a full-scale assault on the Tokyo Settlement after destroying Pendragon. The Black Knights and Autobots, already exhausted from fighting the Britannian forces just moments ago, are forced to retreat to the Ark when they end up losing half their forces.
Furthermore, Zero still disappears from the battlefield, but this time due to being teleported away against his will.
Also, Jeremiah still has his "I'm begging you, please die." moment, but now it's directed at Wheeljack after he innocently questions if this is 'that Orange guy' he'd been told about, as opposed to Zero deliberately pushing the Orange button.
Suzaku still tells someone their very existence is a mistake at the end of R1. Here though, it's directed (very accurately, and rightfully so) at an unaffected Megatron.
Code Prime - R2: Revolution
The Knights of the Round attempt to launch an assault against a new ruler of Britannia, but instead of it being Emperor Lelouch, it’s Megatron following his conquest of Pendragon.
Additionally, while Bismarck has the same last words here as he did in Code Geass canon, Marianne is actually present to hear said words.
Also, four Knights of the Round still partake in the assault like in canon, and three of them remain the same with Bismarck, Gino, and Dorothea. The fourth one is Anya/Marianne, as Monica, the fourth Knight from the canonical assault, defected to the Black Knights after the Black Rebellion.
Mt. Fuji is destroyed by Lelouch like in canon, but instead of being destroyed to cripple the Black Knights and Schneizel’s forces, it’s instead blown up at the insistence of Kyoto to cut off the Decepticons’ Energon supply, and serve as a symbol of resistance against Megatron.
When Lelouch destroys Mt. Fuji, he has his "hope begins now" line from canon, and promising a Heroic Sacrifice won't be in vain. In canon, it was for Urabe after he sacrificed himself to save Lelouch from Rolo. As Urabe is still alive, it's instead for Dreadwing, Cliffjumper, and the other Black Knights who lost their lives during the Black Rebellion.
