Role of stakeholders in Criminal law system

Big-ticket CBI cases, including 2G spectrum allocation scam, coal block allocation scam, Vyapam scam, Virbhadra Singh corruption probe and ponzi schemes like Saradha, are being either monitored or regularly heard by the Supreme Court and several high courts. In fact, in 2G and coal scams, the Supreme Court has restricted all other courts to entertain any application against orders passed by the trial court. This system of monitoring has some problems associated with it. It tends to impinge upon the right of fair trial of the accused. It also impinges upon the independence of the magistrate or other trial judges. My question is: 1. How fair trail of accused in impinged? Isn't adjudication Judiciary's prerogative? I'm definitely missing something crucial. 2. Also in criminal law system, police investigates & files chargesheet. Prosecutors file the case & judges adjudicate. Am I correct? Being a student from non-legal background, am struggling to grasp the concepts. Thanking you in anticipation.