If not Stone then it's Robotnik, who else?
May be he created lot of things before his encounter of Sonic, but hasn't need to use them all until now.
Yeah but... in Sonic 1 we have a scene where Dr. Robotnik is surprised by how much power Sonic's quill has and tells Agent Stone to ready the "prototype".
Then Tom took Sonic to Rachels place and then to that San Francisco pyramid and we see Dr. Robotnik flying the Prototype.
So, the only logical conclusion is that given it was called the "prototype", it was the one-and-only, but Dr. Robotnik decides to build the Egg Mobile during Tom and Sonic at Rachels and despite the Egg Mobile being regarded the successor... goes back to the Eggpod. It just doesn't make much sense to me.