Sage isn’t part of the Eggman Empire. Eggman wants her to have an actual childhood instead of constantly being attacked by Sonic.
Froggy isn’t sapient, and the reason why Big keeps losing him is because Froggy is actively trying to get away from him.
Shadow is autistic, schizophrenic and has severe PTSD.
Sonic and Amy have mutual romantic feelings for one another, Sonic just happens to be more insecure about them than Amy.
Everyone hates Omochao.
Metal Sonic can talk, he just chooses not to.
Station Square wasn’t rebuilt.
Most of the animal characters live in Sunset Heights.
Sonic Colors for the Wii is non-canon (but the DS version is.)