Bury the wirecloth of your run a foot down ... we went so far as to add concrete to the bottom of the trench. We have determined predators.
Run wirecloth around the base of your coop as well - bury it the same way.
We also ran it under the floor joists of the coop above the ground to deter rats from chewing their way up into the coop.
Use removeable roost rods or an angled roost ladder so you can remove or lift them when cleaning the coop.
If possible, place windows opposite from each other for cross ventilation in the summer.
Storage: room for straw, wood chips, bags of feed, dicotomous earth, meds, tools (for cleaning, repair, toe nail trimming, etc), feed suppliments (flax seed, oats, etc). If you are like me, you want to buy in bulk to save money and trips to the feed store. That sounds like a great idea until you have to store it all.
Cover your runs in wire cloth. Then roof that with clear corrogated plastic sheets. It will keep the rain out, provide shade and keep extra litter out. (I do this because our pop door to the coop stays always open to the run so that the girls can go in as late as they want and get up as early as they want. In the winter and early spring, we let them out to free range in the garden, but otherwise, they are kept in the runs.
My runs abut the coop on one side, so have 3 wire "walls". In the winter, I lower a thick plastic sheeting down on the two windy sides to keep the rain from blowing in. The girls love to take their nice, dry dirt baths all winter. AND it makes it much more pleasant to clean the runs and hang out with the chickens.
Run electricity out to the coop and storage areas. Have access to an outlet so you can plug in heat lamps over the roosts in the winter, etc. Have lighting in the coops, storage area and out to the runs. A motion activated light near the coop is nice so that you aren't working in the dark until you get to the light switch. (Helps the kids to feel safer, too.)
Put wire cloth over windows on the outside of the coop (if it is outside the shelter of the run) before attaching the window trim. Keeps them safe and looks neater. The only down side is that you can't clean the windows on the outside with many windows.
Keep a boot tray full of various sizes of rubber boots and clogs so that visitors, friends and the whole family can go out together.
And, I agree that it pays to think ahead. If you leave the possiblity open that you may want to expand your runs or coop, see if you can place your first one in such a way to make that possible in the future. I'm planning my run extension and a small coop for additional birds. I wish that I had laid out my coop and runs differently so I'd have more room. ~Sigh~ Now my kids are teasing me that we'll have to move so I can have more room for my chickens! You know, if the market weren't so horrible, I'd be seriously tempted! LOL