The Supreme Courts job is to determine if something was legal, they were granted the authority by the people. If we want to change that, congress (the people's representation) can amend the constitution.
Congress can also clarify by granted the authority (as the justices explained). At any point in the last 7 years (while this court case has been ongoing), congress could have enacted the laws, they discussed them. The regulations didn't pass. The supreme court pointed that out.
Why would congress put forth these rules if they had already granted the EPA the authorization? -- because the EPA never had such authority.