Sonic the Fighters/WMG

Dr. Robotonic is actually a separate character from Dr. Robotnik.
He was Robotnik's obscure cousin who tried to steal his thunder by building knockoffs of his machinery, including the Metal Sonics and the Death Egg II. This would also explain why he is smaller than Sonic himself in this game.

The Sonic Clone is still alive.
It showed that it survived its encounter with Sonic, agitated, although the fate of it is not shown afterwards.