Just to mention I do squat at home, as I've been following simplefit. However, because my legs are quite strong, I don't think it's having much of an impact considering I can easily do 30 to 40 proper squats without added weight. Hopefully once I get back to the gym I can work out a good strength program again. I'll focus on cutting this summer. I just don't want to lose too much muscle.
Have you tried single leg squats? You can still build a ton of strength with bodyweight exercises just by making them harder.