Warning: Contains SPOILERS for Sonic the Hedgehog 2
Sonic the Hedgehog 2 features Knuckles changing from antagonist to ally, which could create a problem for Sonic the Hedgehog 3. Sonic 3 is set to feature Shadow the Hedgehog, and if the film is anything like the games, Shadow will also be a fierce villain who eventually turns into a friend. This apparent similarity could pose problems for the franchise further down the line.
Sonic 2's post-credits scene sets up Shadow the Hedgehog, the Ultimate Lifeform that has been a staple of the Sonic series since his introduction in Sonic Adventure 2. Shadow is the product of Project Shadow, an experiment put on by Gerald Robotnik in order to discover the secret to immortality. Although Project Shadow occurred 50 years before the events of Sonic 2, Shadow is sure to be back, likely as the villain of Sonic 3.
In Sonic 2, Dr. Eggman manipulates Knuckles into helping him, making Knuckles the big-fisted adversary of Sonic throughout most of the film. By the end, though, Knuckles realizes that he has been manipulated and teams up with Sonic and Tails to take Eggman down. This foe-to-friend arc is very common throughout the franchise, with many game villains eventually becoming good. Alongside Knuckles, Shadow also follows this character arc, meaning that Sonic 2 and Sonic 3 could feature the exact same villain story back-to-back. Since Sonic 2 was accurate to the video games, it is likely that Sonic 3 will be as well, meaning that the repetitive nature of Shadow's arc could hurt both movies.
Sonic 2 differentiates itself from the first Sonic the Hedgehog in a variety of ways, with both films having similar cores but providing wildly different story experiences. By repeating Knuckles' story with Shadow, however, Sonic 3 could be way too close to its predecessor story-wise. Not only would this make Shadow's story seem derivative, but it would also retroactively make Knuckles less interesting, ruining both characters in one fell swoop. Not only is it formulaic, but Knuckles' story simply doesn't work for Shadow's character. Shadow isn't a friend who fights for good like Knuckles. Rather, he is a lone wolf antihero, doing whatever services his goals. If his goals align with Sonic's, then Shadow will help him, but Shadow also has no problem clashing with Sonic. Shadow is a tragic, violent character, acting as a rogue in order to get what he wants. Having him become allies with Sonic, Tails, and Knuckles by the end of Sonic 3 is both a disservice to Shadow's character and a disservice to Knuckles' story.
Although Sonic 3 is way too early to do it, eventually Shadow does need to stop being a pure villain. However, rather than doing it in one movie, it would be better to execute this arc over several movies or shows. With Sonic 3 and a Knuckles spin-off series in the works, it is safe to say that the Sonic series is far from stopping. Having Shadow act antagonistically towards Sonic and his friends over the course of several movies and TV shows would serve his character much better, solidifying his lone-wolf attitude. However, since Knuckles already does the villain turned hero arc in Sonic the Hedgehog 2, having Shadow do the same in Sonic the Hedgehog 3 is a bad idea.