I have thought of a theory. A theory that Sonic and Robotnik (Or Eggman, whatever you prefer) have a relation. And I don't mean that they love each other secretly, so no dirty humor in this theory. Let's dive into it, shall we?
I was searching for random info at Wikipedia when I found an article about Robotnik. In it, a certain piece got my interest. I'm not 100% sure what stood there exactly, but it was something like: "He used to be a good scientist named Kintobor, but after a experiment gone wrong, he turned evil and reversed his name." I speculated by myself what this experiment could be. Maybe it was because he created a potion that turned him evil by accident, or maybe it was because of an explosion that "crazy-fied" his mind.
But then I got to my final thought of what this experiment was: Sonic. My theory is that Robotnik mutated a hedgehog into a more human-like body because he felt kind of lonely and he dind't want human-like chickens, pigs or birds. After Sonic was created, he either: 1: Was evil so he destroyed Robotnik's base and Robotnik started creating robots out of animals to stop him. 2: Thought Robotnik was evil and attacked him, so that Robotnik was turned evil because he hated that what was supposed to be a friend was turned out to be his nemesis.
Sonic, after the events of the best ending possible in the first game, mutated a kitsune by accident, resulting in Tails becoming Sonic's best friend. The rest of his friends like Rouge, Amy, Knuckles, Silver, Vector etc. were mutated later, but not by Sonic. They all mutated by the remaining power in Robotnik's base.
And the final part of my theory: Robotnik wanted to mutate more animals to stop/kill Sonic and co., since robot clones dind't work. That's why he wanted to collect energy from Chaos Emeralds, The Master Emerald and the Wisps. I know that he used the energy for weapons/robots/creatures or whatever, but I also think he secretly wants to keep energy to mutate, but Sonic steals the energy.
Alright, I'm done. I hope you agree with my theory and see ya later.