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In my view, squats are not as total-body as deadlifts. Anyway, best to do both because synergy. Barbell squats are of course the best stressor for building or maintaining lower body strength, but there are plenty of squat exercises in the Calisthenic category that are worth doing in a Calisthenics routine:
Both squats and deads are great, especially as we age. Picking a nit: For me squats are the better whole body exercise - full squats force a greater range of motion than deads. I'm also sore over a larger part of my body after a squat workout.
I'm a big believer in "all the way down". It did wonders for my knees. I'm guessing that going low forces your to engage the entire leg, both hamstrings and quads resulting in good muscle around the knee joint that helps support it. I also do "low bar" squats as they work better for me. If I can't get down, I remove weight.