The problem is with the Special Counsel statute.
It superseded the Independent Counsel statute, which is what Ken Starr operated under during the Clinton impeachment. The "independence" gave the Independent Counsel the power to abuse his authority, which is what many thought happened with Ken Starr.
So they watered it down and created the "Special Counsel" statute, where the Special Counsel would report to the Attorney General. It assumes the Attorney General has integrity and is non-partisan when it comes to upholding the law.
In 2000, they also revised the OLC memo which said that the Special Counsel could not indict a "sitting" President. This created problems in a couple of areas. The Special Counsel could not indict and the Attorney General was left to make the decision, assumed to support the law over politics.
Mueller was given the job with even more restrictions. He was only permitted to look at Russia and who may have assisted them in hacking our election system. His hands were tied from the beginning.
He and his team knew they could not charge a president with anything. They had to turn it over to the AG. So an indictment was never on their menu. Mueller stuck very closely to the rules he was under.