Nonette Enneagram and Monica Krushevsky receive more attention in the story as opposed to canon.
Dorothea Ernst, who was a Flat Character with only a few seconds of screentime in Code Geass, is given character as the most stereotypical of the Knights of the Round.
Kallen's mother, who only appears in two episodes of Code Geass, is given a first name and works on the Ark in R2 as a nurse.
Several Time Skips between Code Geass episodes are shown in R1, encompassing the events of various episodes of Transformers: Prime. Specifically:
The Time Skip between Refrain and Guren Dances encompass the events of Scrapheap, Predatory, Deus ex Machina, and Con Job.
Metal Attraction and Partners take place during the time that passes between Cheering Mao and Nunnally Held Hostage.
TMI and Stronger, Faster take place after Nunnally Held Hostage and before Knight.
Synthetic Energon was ignored after it was first introduced until Season 3 where it played a critical role in restoring the Omega Lock. Here, the Autobots and Black Knights are still looking into using it as fuel while busting out the kinks to allow the Autobots to use it without going crazy. It's later used as a fuel source for a new axe built for Optimus. By the time R2 starts up, the science division has perfected it that it now serves as fuel for the Ark and the Knightmares, though it still can't be used for medical purposes.
Prior to the Battle of Kyushu, Lelouch has a phone call with Euphemia where the latter asks him about why he killed Clovis and learns about recent developments between Britannia and the Decepticons.
In the epilogue of R1, C.C./Cera meets several of the Thirteen Original Primes, who never had speaking roles in Prime.
R2 ends up incorporating characters from every canon element of Code Geass and the Transformers Aligned Universe, along with several Canon Foreigners from Nightmare of Nunnally, Animated, RID 2001, and even Generation 1.
The Protoforms from the Harbinger were only used once in canon to make clones of Starscream. They're used in R2 by the Autobots and Black Knights as the frames for the Shinkiro, the Guren SEITEN, the Lancelot Albion, the Raiden SEITEN, and the Gawain Nerion.
The author explored the Caretaker of Spacetime and the Geass-Skull from Akito the Exiled, making them tied together in the distant past, though functionally very different from each other.
Marianne is given a little more of a deep dive into her past, explaining her reasons for being a part of Ragnarök. Plus, she becomes a recurring side character through the story as a mover and shaker behind the scenes.
In canon, there were four Iacon Relics that had their locations stored in the Nemesis's databanks. Here, there are eight.
Miss X doesn't have very much information in the source material. Here, not only does Nunnally give her a proper name (Misty Ix), but after some time, we find out her secret origins: She's a clone of Marianne and C.C. who escaped.
