I've been doing a lot of work and research on my chicken tractor in the last month.  I've done far more reading up on construction and carpentry topics than I ever thought I would!  My chickens will be living in their chicken tractor full-time, but most of these items apply just as much to a proper coop.

Predator Proofing

 Read enough predator-related message threads on the chicken forums, and you will start to see raccoons around every corner.  Which isn't far from the case, honestly!  Even in the city, chickens face attacks by transient hawks, raccoons, and free-range dogs and cats.

One common lament I've read over and over is, "The [raccoon, dog, cat, whatever] went right through the chicken wire!"  It's often said that chicken wire is only good for keeping chickens in - it does little to keep other animals out.  Hardware cloth, which is made of welded wire in a square grid, is the only predator-proof option.  Neither PVC plastic hardware cloth nor chicken wire will keep predators at bay.

Here's an interesting tidbit I learned along the way: raccoons can figure out how to open most fastenings.  One woman reported that a raccoon on her property learned to open a thumb clip (the kind you find on a dog leash), a clip carabiner, and a twist carabiner.  She finally had to start using a small padlock in order to keep the bandits out.

Access

Learn from the mistakes of others!  I have heard many people regretting their coop designs whenever they have to go inside for cleaning or fetching a chicken.  Ideally your coop will be tall enough for you to stand upright.  Low chicken tractors should have a hinged lid, so that you can reach every corner. 

One woman said that if she could do it over again, she'd put hinges on every plane of her coop, because you never know which spot you'll need to access in the future.  That sounds like smart advice!

Ventilation

Chickens are highly susceptible to diseases brought on by moisture (like coccidian) and to the ammonia fumes from their own droppings.  I have seen many coop designs which look more like dungeons than anything else.  Be sure that your coop design provides for adequate ventilation, to let moisture and ammonia fumes air out. 

I live in the Pacific Northwest, where humidity is high all year long.  Chickens exhale quite a lot of humidity when they sleep, so I can see mildew being a big problem in chicken coops.  I'm planning to over-build for ventilation, then block off the vents or windows as needed later.  It's easier to block off a window than it is to cut a new one on an existing coop.

Poop

One clever tip I've picked up online is to include a "droppings box" in your coop design.  90% of the poop in the coop will fall directly beneath your perches or roosts.  You can make clean-up easier by installing a shallow box which you fill with absorbent bedding like shavings.  You will probably want to lay a sheet of wire on the top, to keep the chickens from scratching around in there. 

Any other suggestions?  Drop me a comment and let me know!