For what its worth, I used to do your standard 3x5 rippetoe style squats, or reverse pyramid, or 5-3-1. I do think it helped overall to give my legs a good foundation of strength. I hardly ever squat now but when I do I retained a good amount of strength.
That being said, for the last year I have switched to single-rep weighted pistol squats. The reason is because my legs got very big with regular squats and my body began to look disproportionate. My body had the V type shape except upside-down. I noticed people began looking at me, and looking right to my legs. It took a lot of focus of my upper body like chest and abs in my opinion.
I worked along side this trainer who had worked with a few clients for acting jobs and what not. He told me as respectfully as possible that my look looked a little sleazy with my legs too big and my upper body too long and lean. He recommended the one-rep pistols and told me I wouldn't miss a beat in strength but I wouldn't put on more size. He was right.
The single rep pistol squats have helped me gain strength in my legs and more importantly gain an athleticism I didn't have before. I was athletic before, but now things like box jumps have gone through the roof and that never happened squatting. I am also happy with the size of my legs so I am glad the single rep keeps it to where I gain strength but not size.
I am much happier without squatting often and feel much more explosive and quick as well. I hope this helps.