My favorite fan theory about Shadow's creation: It's implied in SA2 and confirmed in Shadow the Hedgehog that Gerald visited Angel Island and was aware of the echidna tribes. That means he probably saw this mural:
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Upon recognizing his own likeness, he may have modeled Shadow after the depiction of Super Sonic here. Not only does it explain why he went from a giant plesiosaur to a mutant hedgehog, it explains why Shadow's spines are always super-shaped. Also this quote from the FinalHazard (paraphrased):
Probably nonsense but I like it.