God wants us to PRAY for all men (1) to be saved and (2) come to the knowledge of the truth (1Timothy 2:1-4). This is the fulfilment of the 2 parts of the Great Commission: (1) Salvation thru the Gospel, and (2) Discipleship in God's Word. So the Great Commission must be backed up by Prayer, for it to be fulfilled. So when we pray: "God's will be done and His Kingdom come" for others, our prayers should be focused on the fulfilment of the Great Commission in their lives, that is, on (1) their salvation and (2) their spiritual growth.