Sonya is a boy and Manic is a girl.
The Oracle set it all up for his own twisted amusementAleena wouldn't have abandoned and split up her kids at all if he hadn't just appeared one night and told her that they had to be split up to reunite to form the Council of Four to overthrow Robotnik.
The show wasn't originally going to be a Sonic cartoonSimple, and it makes sense, given how different it is from other Sonic media. Early in development, it was originally going to be a wholly original cartoon, only to be Re-Tooled into a sonic show. It is entirely possible that originally the heroes were just a Brother-Sister Team consisting of the characters who became Manic and Sonia, given sonic's personality is still relatively intact. Robotnik was likely some generic evil overlord who the two main characters would use the Power of Rock to fight.