Chaos did nothing wrong

No joke, making the Echidnas the main villains could legit make the Sonic timeline work in a movie series. In no particular order:
- Sonic is a creature empowered by the chaos emeralds, this is the reason the Echidnas are after him, they view him (or whoever empowered him) as a thief.
- The Echidnas could either be tricked by Robotnik, or be the ones he captures to power his drones. In the latter case, they are some of the many creatures Robotnik has captured for his goal of taking over Sonic's world. If Robotnik learns of the true source of these creatures' power, it will plant the seeds for Chaos after his defeat.
- Knuckles as a major antagonist, he is empowered by the emeralds to try and finally capture Sonic. Key details are hidden from him (perhaps that Sonic didn't actually steal the Chaos energy himself, or that Sonic was responsible for Robotnik, perhaps both), and when Knuckles learns he was lied to, he becomes an ally. The Echidnas are finally defeated.
- The remainder of the Echidnas form one last ditch effort to defeat Sonic, but Robotnik sabotages this, sending the emeralds to Earth. He follows, with the creature the Echidnas made to defeat Sonic, with the goal of taking his revenge on the Earth.