Discrimination
Sonic always knew Shadow was feared for his great power, especially after the black arms fiasco. Times long passed, but the fear remained. In the not so subtle ways other would hold their children closer, or the glares and cautious glances aimed towards him. Birthed through creation being the only thing changing their pity to fear. GUN kept a short leash on him per the publics demand. Sonic knew discrimination wasn't the way to go, it was wrong. Shadow wasn't as bad as most made him out to be. He knew his heroship was going to be questioned once he admitted to dating and falling for Shadow. They judged him and looked with disbelief, creating rumors and fabricated stories. Sonic didn't mind he still continued saving the world and fighting Eggman as always. He just wished others would look past Shadows differences and see him for who he was in the inside.