Sonic is not perfect at all, while he always tries to do good on his adventures he's suposed to have an elevated ego, sometimes he let his friends behind to do his own things. And he always does things without thinking the consequences of his actions. A gary stu is a perfect character, who doesnt have any kind of imperfection and everyone loves them.
Knuckles and shadow opinion of sonic are the perfect example of people pointing sonic imperfections as a person.