So like, is Sonic Team just trying to ignore the Chaos Emeralds (even in games like Forces where it makes no goddamn sense for them to not be at least mentioned) because of the 2000's where they were the solution for every problem?
They went back to being a game mechanic instead of a plot element. I didn't mind this change but I think with a situation as dire as Forces pushing them to the background causes problems with the story.
I think they were probably just lumped together with the rest of the series story content that was left behind at the start of the decade. Sega and ST obviously wanted to dumb downsimplify things and they were more than likely just a casualty of that a lot of the time.