Keep Wade’s dad storyline, but he’s now a professional boarder.
Wade wants to beat him for the same reason.
The gun agents have no ties to the eggman rip off. Instead they are involved in a plot to infiltrate the area this bordering tournament is in for something that will help them find shadow.
Knuckles has become accustomed to extreme sports as it brings out his warrior side.
He teams up with Wade to train him to compete or maybe he trains Wade for a potential future GUN invasion.
They get themselves caught up in GUN’s current plot, perfect time for their training to be put to the test.
Knuckles and Wade actually can fight together and kick The gun agents ass. Learn something to setup sonic 3, that isn’t key to the movie plot where you don’t have to watch the show to understood the movie. Just a fun bone to throw to fans waiting for the sequel.
Knuckles and Wade realize that even though they’ve both been left behind by their tribes, they can actually work together to stop future conflicts that will leave more people abandoned. Knuckles sees the beauty in the planet and how it can actually still enhance his warrior attributes, while also being able to learn to appreciate his life and its potential. Knowing that he will still always have a family even if he doesn’t have a true “home” . With a family being his home.
Something among those lines.
I think this way, you can take something fun from the games, really connect the human and alien buddy cop angle, and have a relatively emotional story, and setup the third movie, without it needed to be a big deal, but a fun payoff for fans.