Running is well documented in its role in improving bone density: http://healthfully.org/highinterestmedical/id33.html
Unlike weight-lifting there are actual studies showing running promoting neurogenesis (the increase of brain cells) and improving performance: https://www.google.com/webhp?sourceid=chrome-instant&ion=1&e...
Finally, muscle mass is far from enough to be an effective metabolic regulator. While I have yet to meet anyone who runs 100 miles a week and is overweight, it's not uncommon to find that someone who benches 500lbs still carries a gut. I myself have gained a great deal of both fat and muscle since my school years when I was a runner.
I think weight-lifting does some great things depending on one's aesthetic goals, and it's probably the most time efficient way to increase bone density. It's hardly the optimal exercise for general health, though. There are many aspects of health, ranging from neurogenesis to heart health to immune system function to maintaining telomere length that cardio most helps.