I think that the problem with human is Sonic's world is more the art style and general design problem, which lead to something that doesn't look cohesive. Eggman always make sense because he's humanoid, but his general body shape isn't actually realistic. It doesn't really work with Princess Elise because she looks like an actual human, there's nothing surrealist about her design, which contrast to the Sonic world too much. This can also be applied to both characters personnality. Eggman is evil, narcisstic, arrogant, intelligent but immature. He's not suppose to be relatable, because all those traits are exagerated too. Elise is sweet, kind-hearted, anxious. These are more relatable traits, and they're never extremely exagerated. While making a character relatable is positive in other game or other context, it doesn't really work to have a normal human in a world where everything else is surreal.