Simple solution.
You want, and need, the full range of motion and stabilization you can only get by squatting freely. If you want to have a nice looking body then just stick with machines. But since you voice this concern I assume you want something more functional, you want strength and core strength.
Well you're in luck my fren! Just like smith machines were invented to strip out a good portion of the work, so too were squat racks. That's a bit of an exaggeration. Anyway.
Front squats (back squats are for weak people and cheaters! haha). So you can clean the bar and front squat or you can use the bench racks to pick up the bar in the racking position. Be warned, you will become addicted to front squats.
Another option would be to stand in front of a bench with your back to it. Raise one of your legs behind you and place your instep on the bench. From there do a 'one legged' squat. You can hold dumb bells. This is a great exercise because it is unilateral.
Also, there are a whole range of o lifts that you can do that will improve your over all performance and enjoyment in the gym. Obviously with these lifts you wont lift the same max
weight but you will develop more functional strength than the back squat.