I like to use pause squats for 2 primary reasons:
1. They really improve postural strength - for people who tend to lose their posture coming out of a squat, including knees going valgus, back rounding, etc.
2. They help strengthen the very bottom range of motion, which greatly helps the pull from the floor in the sn and cln, and also gets bouncy lifters stronger (i.e. lifters who bounce really hard in their squats - often this precludes them from developing balanced strength in the full squat rom).
So i use them with certain lifters when we need to correct that stuff, or I may use them with people who haven't demonstrated a particular need for them if we're doing a squat strength emphasis cycle.