The super Emeralds' only real issue is that we already have an implementation of them implying that they are directly related to the Chaos Emeralds, otherwise you could make up any new excuse and it would stick for how it's always been. You could treat them like the Black Star Dragon Balls from Dragon Ball GT, where once they're used, they're spread across the universe, and that's the reason we haven't actually seen them since, so to bring them back would mean actually finding them for one reason or another, and an excuse to actually go to space this time. Idk. I don't think it would matter much more than it does now in terms of power scaling. It's just something that would be neat to see reinterpreted (Personally, I like the idea of having multicolored lightnting glowing and reflecting off silver colored fur) even if it was just once again. Idk why Flynn would mention that. I'd rather he never say never.