Watching some of the
Hellfire Commentaries playthroughs of some of the Sonic games, they expressed the view that Shadow being created by the Black Arms (and thus making him a
Half-Hedgehog Hybrid) was really stupid and not needed... but at the same time, they puzzled over how Professor Gerald, in his experiments to make the Ultimate Life-Form, went from The Biolizard to Shadow, with no other prototypes in the middle. That's when I realised that him being created by the Black Arms was
actually necessary to explain why Gerald made the technological leap that he did: using his own intelligence and resources, the best he could come up with was the Biolizard, a creature which clearly wasn't up to scratch. At that point, he encountered the Black Arms, and they gave him the information and resources he needed to create Shadow — they actually say in the game that "He needed a little help", so they helped him out. The game
Shadow the Hedgehog basically explains every plot hole from
Sonic Adventure 2, both why the Eclipse cannon was made and how Shadow was made (sorry,
Hellfire Commentaries - no offence was intended).