Considering all of the positive points you made regarding riding the bike, I wonder why you are torturing yourself by running... unless you like that kind of thing.

Cycling is better for your knees and ankles (low impact), and depending on how far, and how hard you go, great cardio.
You spend a little more time riding for the same effect ( I believe 10 miles of hard riding = 6 miles of running +/-), but the chance of getting "shin splints", or "achilies heal" on a bike? ... not likely. Ride on... ... ...