Where are you located? It can help to know what extremes you are looking at in summer and winter.
Anything that touches the ground needs to be protected from rotting. That might be treated wood, cinder block, concrete, whatever.
If your run is covered, you need to be able to walk in there without bending. I don't know enough on how many chickens you plan to have, your flock make-up, your climate, how you will build the run, and such to comment about size.
If your lumber is 16' long you might be more efficient if you build it 8 feet wide, not 12. Less cutting and waste, though some of that cut-off can be used for nests and such. Though how you build your roof plays into it too. You need enough slope for water to run off and maybe leaves or snow to slide off. I personally like overhang so you can leave the top of the walls open for ventilation with the overhang keeping rainwater out. If you build a single-slope roof, the wider the span the larger and heavier the support beams need to be. In a truss-type roof you can use smaller lumber but the span is still important. They are more complicated to build and they still need to handle wind load, plus maybe snow, ice, or leaves,. Whether 8' wide or 12, the roof will be important.
As far as location, do not put it where water drains to it and stands. Put it where it will stay dry. To me that is the main criteria for location. Anything else can be dealt with.
You need enough natural light in there so you and the chickens can see what you're doing. If you leave open space up high for ventilation (covered with hardware cloth against predators) some light will come in from that. You can put in real windows (maybe get some cheap for Craigslist or a rehab store) or you can make windows by framing in Plexiglas or something like that. In the southern US I like the windows on the cooler northern or eastern sides. In the cold north you might want them on the warmer southern or western sides. I personally prefer the coop a little darker, cooler and more soothing. Some people like them bright as the blazing sun on a white beach. I don't know that it really matters that much, but you and the chickens do need to be able to see,