Honestly, I just take the Super Emeralds as Super-Charged Chaos Emeralds. I might have liked an alternate explanation, but it doesn't bother me nearly as much as other retcons, especially since Sonic Adventure brought the idea that the Chaos Emeralds were once quite a bit larger 4,000 years ago. I don't mind retcons when they make some semblance of sense. But the Sonic X thing? No. It conflicts with the game canon anyway: feel free to make sense of Shadow's story if it's shared between Sonic X and Sonic Heroes/Shadow the Hedgehog. Then again, they're forcing the Two Worlds Scenario down our throat, whether we want it or not.