Substitute is an option for Mismagius because said move protects Mismagius from Pursuit attempts, as well as debilitating status, like paralysis or poison. You just have to predict when you use the move.
Alternatively, if you're using Substitute + set up move, you try to bring in Mismagius on an Pokemon it can force out. As the opponent switches, you set up a Sub. Then as the opponent attacks the Sub, you Nasty Plot/Calm Mind up. Then you're free to either attack or set up another Sub.