It's the most written and talked about "exercise"!
Done properly...it's the most efficiant and effective body builder, done poorly the most efficiant and effective body wrecker.
Learn the squat, but learn to master it on your own terms, master it and it will become the key-stone to your workout.
You need to work out your own style and not let people tell you how to squat unless they have taught many with success and by success I mean no injury.
This is rare, so teach yourself.
The reason why this exercise is SO uncomfortable is purely because it is stimulating a LOT of muscle AND it's not just the muscle tissue that is under enormous stress but the whole endochrine system.
I've been consistantly squatting for roughly thirty years now, the one mistake I made early on was trying to train to become a draft horse and not knowing that I'm neither that or a racehorse.
It took a while to find my training style, the wrong type of work was causing too much soft tissue damage.
Interestingly, Squatting for thirty years doesn't make me an expert on teaching this exercise, all I can give people is what works for me.
It's one exercise I would not attempt to teach.