I don't the Freedom Fighters are no longer canon to the Sonic lore. However, they already made 3D concept art of the characters. Plus, we did get that cameo in Sonic Forces: Looming Shadow.
I know they were only included as merely Easter Eggs. But there could be a possible chance they can be canon. My suggestion: reboot them again. The best way to add them to the story is seeing how they were 'not' in the story. The world of Sonic the Hedgehog has a lot of amazing places. But the one place that hasn't been explored is Sonic's birthplace, Christmas Island.
According to Sonic himself, it is a strange place, much different than anywhere on Earth, filled with strange robots and animals. I figured it to be based out of the worlds from the early Sonic cartoon. So I figured Sally Acorn, Nicole the Holo-Lynx, Rotor the Walrus, Bunnie Rabbot, and Antoine D'Coolette are all childhood friends of Sonic (BEFORE the games). Sally could still be royalty there, Nicole's origin can still be relevant, Bunnie could have gotten her robotic limbs from an incident at a young age, Rotor specializes in technology powered by Power Rings, and Antoine could be once a romantic rival of Sonic's for Sally affection.
In their pre-teen years, Sonic started to get bored of the living on the island, despite being in a relationship with Sally. But all that changed when one day, a man named "Dr. Ivo Robotnik" attacked all of Christmas Island. He came to the island decades ago to study their strange technology, and has returned in his quest to conquer the world. Sonic, Sally, and the rest of their friends fought back against Robotnik and drove him away from the island. Inspired by the event, Sonic decided to leave Christmas Island to go see the world and satisfy his never-ending thirst for adventure, while Sally and others stayed complete their lives. So Sonic took his new plane, The Tornado, and left home, where he would later run into Robotnik again, in the Green Hill Zone on South Island.
Meanwhile, Sally and the others remain on the island, improving themselves into the Freedom Fighters we know today. Sonic would visit on curtain occasions. Sometimes he brings his new friends and tell his old friends about his adventures. They inspired them to go out into the world and have their own adventures, to do some good everywhere. They even consulted for G.U.N. when it was still active. The more Sonic saves the day, the more Sally notices she and the rest of the Freedom Fighters seem insignificant to him now-a-days. She also noticed how close he was getting to one of his friends, Amy Rose. Sally seem happy that there is someone in Sonic's life that could really fulfill keeping him on the right track of who he is meant to be, as she did long ago. So one day, she official broke things of with him, and started a new path.
The Freedom Fighters can go on secret adventures outside the modern Sonic content. They'd battle enemies that really made any appearances; like Fang, Witchcart, and Lyric. Even team-up with unseen and classic characters; like Sticks the Badger, Mighty the Armadillo, Ray the Flying Squirrel, Honey the Cat, Trip the Sungazer, and even Bark the Polar and Bean the Dynamite.
Plus, it might improve the world of Sonic the Hedgehog by adding a more competent and organized group, since characters have no idea what they're doing anymore in the IDW comic series.
