The funny thing about Sonic Adventure 2's story is that nearly all of its contradictions are tied to the old heroes. Even the stuff off about Eggman save his apparent failure to look into Rouge depend on his history with Sonic. But the instant Sonic or his friends are involved, shit falls to bits.\

That would certainly explain much of why Shadow's story is so beloved; specifically isolated from the rest of Sonic, including it being a rehash of Chaos's story in Adventure 1, it's actually well done. Rouge could've been the one to trigger Shadow's true memories and shit would've still worked.\