I've had knee issues all my life and have always done squats. Granyed all knee issues are different, mine are bone on bone..no cartilage. I've had to change the amount of weight I use, anything over 275 makes my knees scream for days so I've also had to change the way I squat. I now do very slow reps to parallel, then up halfway, back down then all the way up for 1 rep. Do this for 4 sets of 10 and your legs are fried! Also have you tried bulgarian split squats?