If you're supersetting dynamic lunges with step-ups, trust me, you won't go home thinking you needed to add or sub in squats.
Because of my knees, I do step-ups on a low step, so I get a little more aggressive with loading. It ends up being a lot like a unilateral squat. You're stepping up instead of squatting down, but the muscle use is going to be pretty similar, as long as you push off the heel of the foot on the step, and don't push from the floor with the other foot.
While I don't think there's ultimately a big difference in muscle development, it feels to me as if I'm getting more work from the adductors (inner thighs) with the step-up than with the squat. The hard work of spinal stabilization falls to the outer hips and thighs on the squat, but on a step-up, your body has to prioritize balance, and there's probably some internal rotation of the hip to achieve that, firing some of the adductors.
That's just a guess, of course.
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