These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Sonic's defeat of Robotnik here counts too, as it's one of the few times that he used his brain to defeat Robotnik, simply by appealing to his vanity & new found god-hood by pointing out that if Robotnik was so powerful, it wouldn't matter if Sonic had an ally or not, Robotnik would still win. Robotnik buys into it, and lets Sonic choose one person - Sonic chooses Knuckles, the Guardian of the Chaos Emeralds, who promptly uses the Grey Chaos Emerald (The "control" emerald) to defeat Robotnik.
The reason they defeated Robotnik to liberate Mobius counts here too, as the Omni-Viewer states that Super Sonic will cause a planet-wide EMP when he explodes the asteroid he was trapped in. Sonic immediately asks the Omni-Viewer if he can move the asteroid above Mobius, and when asked why, he simply smirks and says "Because most of the technology on Mobius is Dr Robotnik's!"
Fan Preferred Couple: Both Tekno and Johnny are more common love interests for Amy than Sonic. Amy likewise for Tekno, who is supposed to be paired with Shorty
Fanon Discontinuity: STC had its fair amount of bad strips that fans would rather forget, such as Bravehog, The Trickster and the biggest stinker of them all; Amy's Secret Past which had no regard for continuity whatsoever. Ugh.
Surely Bravehog was the bigger continuity criminal, totally overriding Sonic's backstory? Its art was significantly worse than Amy's Secret Past, too.
Ironically, those two also contradicted each other: Amy's Secret Past was an attempt to explain why she has similar slicked-together spikes as Sonic despite not having superspeed (him having obtained them during the accident which gave him this) while Bravehog showed all the hedgehogs in the past looking like Sonic.
Draco in Leather Pants: Super Sonic is the most well-known character from this comic, and is the one to get the most love. While people often play up his craziness, also expect to see it toned down often.
First Installment Wins: Very few of the other comics are remembered. Then again Sonic was the basis of the pun in the title, the magazine mostly revolved around him, and his story got all the plot development.
Growing the Beard: The original issues were mainly crude one-shots with little continuity and often horrid artwork. It was also more comical then later issues. At issue 8 is when they decided to gain an actual plot, though even then it took a few issues to fully grow its beard.
Jerk Sue: Sonic, according to Word Of God- Nigel Kitching has stated in-interview that Sonic being mean to Tails and getting away with it was very much his intention.
Narm: Shortfuse's aforementioned habit of explaining his origin in every single appearance gets this way after a while.
There were several examples in the non-Sonic stories as well. From the Eternal Champions strips there was Xavier's frequent battle cries warning his foes to fear "the power of magick!" only for it to very rarely work.
From the character guide included in the Eternal Champions special issue each character has a profile which links their greatest fear to the cause of their death, so Trident (who was crushed by a pillar) gets "unnatural fear of pillars" while Larsen (who was killed by his boss, Mr. Tagliani) has "an unusual dislike of tagliatelle".
Tear Jerker: For some fans, the Christmas story which sees Robotnik visited by Father Christmas, who warns him that his downfall is approaching and encourages him to change his evil ways, reminding him that he hasn't really benefited personally from his rulership of Mobius. Robotnik orders him to leave before realizing that he was right: "Keep your advice, old man! I like being evil and I don't need presents! I'm in charge! I've got power! I've got... I've got... I've got no friends on Christmas Day..."
Johnny's death. It still haunts many fans to this day.
Unpopular Popular Character: Tails. His vocal fanbase led to his solo adventures in the Nameless Zone and as 'Zonerunner' in the Chemical Plant Zone, even though he was as hapless as ever and usually triumphed by accident.