About Sonic Prime, there's one element that I think was constantly not good, Eggman. Eggman here feels like the joke character that people mostly think that Eggman always is without any cool factor that the character really has.
Considering that this year we had Super Jim Carry Eggman, Eggman getting serious and physical on IDW, and the sentimental Eggman in Sonic Frontiers, it's a bit sad that Sonic Prime ended up as the only product of the year with a subpar Eggman.
They could change it in the next episodes, but I don't think so.
The way I understood it from the series, I guess that what happened is that the prime universe became "fragmented" as light passed through a crystal and everything in the world got divided into different parts of themselves across the Shattherverse, maybe Eggman being very close to the explosion meant that he got divided into the same world as the different members of the Chaos Council, while everyone else got fragmented into different worlds.