i think that its all about variaty, to never let your body adapt to any kind of training completly. to always be a step ahead.
at one point i was doing heavy fully body workouts 1x a week, then i brought the intensity down a bit and started doing them 3x a week, after that i was doing max-ot based workouts, now im doing crossfit... and so on.
one thing i will say though. my knees have always been chronicly sore (exessive snowboarding for 11 years) and when i work my legs 3x a week my knee pains go away completly. if i
stop working out they come back with a vengance, on a one body part a week program i have limited pain, but its there. no idea why this is but thats where 3x each muscle a week helped me the most.
just dont over train. its so easy to do working each muscle 3x a week..