Their has been a long struggle the Archie comic seems to have been unable to do no matter who the writers have been that I feel SatAM captured. We have never really seen Eggman's control over Mobius having any legitimate weight. Since Sonic is always written to win all his battles and Eggman to be a buffoon, how he is able to keep a tight grip over Mobius is never really shown. Yes he has his egg legions and egg bosses, but that feels more of extortion than having a military stranglehold. Eggman in the comic is supposed to have a massive army spread across the globe that the Freedom Fighters choose to go after the most relevant areas. But yet, because Sonic must always win he never encounters any resistance for Eggman's army. Nobody is ever able to push Sonic back or make him work hard for a victory. The only time Sonic ever really struggled against Eggman was issue 175 where he blew up Knothole and had a robot strong enough to repel him.
This in turn makes Eggman a rather boring character since he continues to unimpress as a legitimate threat in a ongoing series.
But the problem with a weak villain isn't just with Eggman, it seems to affect all other villains the comic has. Naugus has always been treated rather unfairly and is never able to put up a good fight for Sonic and his friends despite all of his magic and sorcery. He makes really stupid mistakes that seem to exist just to give the heroes an opportunity to beat him, rather than them exploiting some weakness in his abilities. Then their is the problem with the chaos emeralds that seem to always grant an instant victory whenever in use.
The solution to this problem I feel would be to make Sonic's victories much smaller as to not undermine his status as a hero, but to also not completely bulldoze any opposition his enemies might offer. The villains themselves would adapt to Sonic and respond to his victories to make future campaigns uncertain, or at the least more difficult for Sonic. If Sonic can march into Eggman's home at any point and slap him in the face then why bother pretending he has any power?