I guess you can chalk up many of the show's inconsistencies to time travel paradoxes. Or even entire continuities, for that matter.
On one hand, you have the original timeline in which King Acorn survived Robotnik's coup d'etat and became a renegade and operative for the Freedom Fighters - as seen in "Sonic Boom". But then you have the timeline in which the time-traveling Sonic and Sally intervened with said events, thus preventing King Acorn from ever escaping and the events of season 2 occur.
If you go further back to when Naugus takes on an accomplice, he can take two possible options: Robotnik or Kodos. If he chooses Robotnik, the events depicted in SatAM unfold in which he seals Naugus inside the Void. If he chooses Kodos, Kodos tries to kill him but Naugus flees into the Zone of Silence instead - leading to the Archie continuity.
If we prevent the Great War from ever happening, things happen quite a bit differently. Instead of marrying Bernadette, Jules might've married Queen Aleena of Mobodoon instead, leading to the events depicted in "Sonic Underground".
If we prevent the creation of Angel Island, we get Planet Freedom from the OVA. Without an island to protect, Knuckles uses his emerald-tracking instincts to become a treasure hunter and both the Mobians and Overlanders live in harmony (except for Robotnik and his Shadowbots).
And finally, if we prevent the Xorda invasion of Earth, we're left with the future Earth of either the official games or the reboot Archie comics.
At least, that's my theory.