I wrote last year about the potential problems with heavy squats. After thinking about things more and doing some reading, I see even more drawbacks from doing weighted squats.
In this article(pdf), Gray Cook talks about the squat and the deadlift. He concludes by saying that a person should "maintain the squat and train the deadlift". In other words, a person should work on maintaining the mobility necessary to do an unweighted squat movement. For lifting weights, a person should focus on the deadlift.
I see this differential in my toddler as well. Toddlers squat constantly, but it is all "mobility" work. The squats are done for the purposes of movement, not for the purposes of lifting a weight. If a toddler wants to lift a weight, they shift into a deadlift position.
It's probably been about a year since I've done weighted squats. At this point, I have no desire to go back to them. I am content training the deadlift as the main lift. I know squats have been utilized in weight programs for decades, but that doesn't mean that they are necessarily 100% healthy.
Sometimes traditions need to change. The combination of squat mobility and weighted deadlifts may be superior to doing both weighted squats and deadlifts. This would be a good topic for a research study!