Squats - Free weight vs body weight
What is ideal?
It all depends on what purpose you are training for. As long as there is a level of overload and increased resistance you will be able to elicit a training effect.
If you're looking to build pure strength and size you should go down the path of free weight.
However if you're looking to develop endurance and are not focused on size, plyometric and body weight exercises will be more than enough.
But be prepared to but in the same intensity and amount of work if you want to progress.