I never will understand this.

Some of Shadow’s original design concepts looked more like Sonic. That’s likely why they did it for SA2 in the first place. And season 2 of Sonic X was a retelling of the adventure games plots, so they had to follow some plot beats

Thats true, I know, But the whole point of SA2 and Season 2 of X was Shadow framed Sonic and Everyone thought He was sonic because of his looks, Even though if you really know what to look for its easy to see the difference.

A fun conspiracy I heard is that G.U.N. was able to distinguish between Sonic and Shadow the whole time. But in order to cover up their heinous actions on the space colony ark, they wanted to keep Shadow’s existence out of the public knowledge. So, G.U.N. influenced news sources to lie and tell people that it was Sonic.