General Ironicus liked Mil, due to how he looked like a human Sonic OC. It got to the point where Ironicus was calling Mil "Tails" in the last few parts.
The student known only as "Goth" is also pretty popular. As stated in Chip Cheezum's riff, at least he actually does something different instead of punching people right away.
The Bald Teacher from the first season has also gained a following, mostly because the person voicing him was named Sephiroth in the credits.
Growing the Beard: The series has a lot of Early-Installment Weirdness in the early episodes, particularly one where a couple of VERY poorly drawn characters start fight that's so weak Ghai lampshades it.