I love Jim Carrey as Dr. Robotnik in the films as much as the next guy. It's just the ending of Sonic 3 implies his demise more heavily than it did in Sonic 2. So, why not give Dr. Robotnik a break and let Neo Metal Sonic take the lead as villain?
Plus, it would be an awesome mid-credit tease if Dr. Robotnik is revealed alive.
Big stars like Jim Carrey, Idris Elba, and Keanu Reeves do contribute a lot to the movie success to non Sonic fans.
If Jim Carrey is gone, they're gonna need another big star to replace him.
Sonic characters alone aren't gonna do much to attract non Sonic fans to watch.