There are a lot differences between General Musharraf and General Raheel Shareef.
Gen R.S conducted his tenure professionally like few COAS's of the 90's. He was exemplary in setting standards focusing on the ground realities, improving outcomes for Pakistan mired with extremism and planned internal security efforts. Pakistan witnessed a slump in terrorist-related activities within the country compared with the previous years, seeing 45 percent fewer attacks and 38 percent fewer deaths due to terrorism with him as COAS. Seamlessly initiating the operations of CPEC was another step and setting up LID structure for security. This was a new type of formation in the Army. Above all, no political ambitions like Musharraf. The operations started by Gen RS faced lesser scrutiny (internally and religiously) as he handled the MO Dte and political figures quite diligently than Musharraf. Gen RS also brought back Army's reputation in good graces that had been flawed by Musharraf. These are just a few things, Gen RS did many more. Regarding Musharraf, he had positive aspects but his political ambitions ruined Pakistan and Army.
The professional conduct of COAS is based on many merits, including handling of military and security situations, expansion of forces, acquisition of newer weapons etc.