Sonic the Hedgehog 2 seems rather loyal to its source material with the characters and backstory. Like most movies, some writing choices have been made to fully separate itself from the games and other Sonic the Hedgehog franchise-related materials, such as the comics. One aspect of Sonic the Hedgehog 2 that received praise was its portrayal of Knuckles the Echidna, a longtime rival of the blue blur himself.
Over the years, Knuckles' character has undergone a steady change. He had a temper, but he wasn't always someone who flew off the handle like his Sonic X counterpart. He was gullible, but he wasn't ignorant like in the Sonic Boom universe. Knuckles' character received praise in the Sonic the Hedgehog 2 movie because it seemed like a "return to form" for a beloved character. Paramount Knuckles is an honorable warrior, and while he maintains his naivety, he's still a character that viewers can take seriously throughout the movie. Despite this, there are a few differences in Knuckles' history that fans are going to either like or dislike.
5 Knuckles' Father And Tribe
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The Sonic the Hedgehog video games have kept Knuckles' past shrouded in mystery. For a long time, all fans knew of Knuckles was that he was the last of his kind and the guardian of the Master Emerald. It was never shown on-screen who Knuckles' parents were and if he had any siblings. It wasn't until Sonic Adventure when the franchise dove into the past and unraveled the history of Knuckles' ancestors. This is completely averted in the Archie Comics, where Knuckles is given an elaborate backstory that is far removed from the game canon.
In the Sonic the Hedgehog 2 movie, viewers get to see Knuckles' tribe and his father in a flashback. Knuckles' father, who bears a similar appearance to Pachacamac from Sonic Adventure, stopped Knuckles from joining him in his fight against Longclaw. The day his father left to fight Longclaw was the last time Knuckles saw his father and his people, thus starting a resentment he'd harbor towards Sonic the Hedgehog for days to come.
4 The Echidnas Vs. The Owls
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In the Sonic video games, there is no mention of an Owl Tribe that opposed the Echidnas. There is the Nocturnus Clan from Sonic Chronicles: The Dark Brotherhood, which once opposed the Echidna Clan/Knuckles' ancestors. However, it's often debated among fans whether Sonic Chronicles can fit appropriately into the timeline or not.
The movie reveals that there was a long conflict between the Echidnas and Owls. This is shown in the first movie where Longclaw sends Sonic to earth via the warp rings to get him to safety. It's further elaborated on in Sonic the Hedgehog 2, revealing that Longclaw was part of a group of Owls that fought to keep the Master Emerald from the Echidnas due to the Master Emerald's incredible power. As such, Knuckles has a distaste for the Owls that isn't present in the games.
3 Knuckles & The Master Emerald
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Fans of the series know Knuckles is the guardian of the Master Emerald, but the reason why he was their guardian wasn't explained until Sonic Adventure. For starters, the Master Emerald does not "house" the Chaos Emeralds, and its entire existence is why Angel Island, Knuckles' home, is able to stay afloat. The history of the Master Emerald goes back 3,000 years with Pachacamac and the Knuckles Clan. Pachacamac led his people to raid the altar of the Master Emerald to steal its power before anyone else stumbled upon it.
Tikal the Echidna, Pachacamac's daughter, tried to stop him, but was unsuccessful. Amid the conflict, many Chao, who lived in the altar of the Master Emerald, were injured. This sparked the ire of the Chao's guardian, Chaos, who turned into Perfect Chaos and destroyed the clan. To stop his rampage, Tikal sealed herself and Chaos within the Master Emerald. Thus, the reason why a Master Emerald guardian exists (i.e: Knuckles) is to prevent history from repeating itself.
The lore behind the Master Emerald in the movie is very different. The emerald was created by the Echidna Tribe using the power of the Chaos Emeralds. Because of its tremendous power, the Owls sought to keep it sealed away from the Echidnas, sparking a war between their clans. At the start of the film, Knuckles has no idea where the Emerald is, but he does know that Sonic is the key to finding it.
2 His Alliance With Robotnik
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In Sonic the Hedgehog 3, Knuckles meets Robotnik shortly after Robotnik's battle with Sonic. The Death Egg crashes into Angel Island and the Chaos Emeralds go missing. Robotnik lies to Knuckles, claiming he's a researcher on the island and that Sonic is evil and trying to steal the Chaos Emeralds for himself. Knuckles believes this, thus allying himself with Robotnik for the majority of the game.
The movie Robotnik meets Knuckles when a portal opens on Mushroom Planet. Robotnik and Knuckles' alliance is initially formed out of their mutual dislike of Sonic until Robotnik learns about the Master Emerald. Robotnik betrays Knuckles, but he suffers a defeat by Sonic in the climax of the movie. It should also be noted that Knuckles saw Robotnik as a friend, and was ultimately hurt by his betrayal before teaming up with Sonic.
1 Knuckles' Reputation
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The Knuckles in the game is a loner, living isolated on Angel Island because of his role as guardian. When he meets Sonic and Tails, they have no idea who he is - and vice versa. It's implied that Knuckles didn't travel away from Angel Island because he had no reason to do so. In fact, it's likely the first person Knuckles met in a long time was Robotnik, thus making it easier for him to be tricked.
By contrast, the movie lore refers to Knuckles as "the strongest warrior in the galaxy" because Knuckles has quite literally traversed the galaxy in search of Sonic. When Sonic asks Tails who "Clifford the big red rage monster" is, it's made obvious that Tails knew of Knuckles prior to meeting Sonic, unlike his game counterpart. In short, movie Knuckles has a reputation as a powerful warrior, while game Knuckles has less of a worldwide reputation in-universe.