I've been a fan of weighted step-ups for a long time, although they've never been my primary exercise for a few reasons - mainly powerlifting and ego. I found this cool article that talks about the benefits of step-ups and how they are better for athletes than squats. 

http://www.overspeedtraining.com/legsart.htm

We don't know what our limits are, so to start something with the idea of being limited actually ends up limiting us.
Ellen Langer