I'm also interested in what you said about the bar hurting your traps. When people start lifting, the bar always hurts them at first, even if the bar is held in a good place. That's why every gym has that retarded pad. It goes away after a bit if you just push through.
Unless you have a preexisting condition you didn't mention, there's no reason you can't work on what's keeping you from performing the back squat.
That being said, the front squat is a great movement, and front squats combined with deadlift variations will give you just about everything you need for lower body development. Truth be told, however, the back squat is the king of lifting movements for a reason. It gets EVERYTHING.
Current PRs at 242- 495, 345, 585, 1425