Vinyl flooring (can be super cheap, even a remnant) makes clean up much, much easier. A long door along the floor on one side, if not just make one side a door, to help with removal of soiled substrates and otherwise necessary cleaning and upkeep. For bedding, I use a lot of Stall Refresher/Sweet PDZ, in addition to a lot of pine chips.
Put roosts in. Everyone has favorites; I use 2x4s and keep them at the same height to avoid squabbles. Put in a door for the birds--cab be as simple as another similarly painted piece of wood with an eye and pulley system to be manually raised each morning.
Raise it off the ground and surround it with hardware cloth to keep pests and predators from getting in, if it doesn't have a "fixed foundation" of, say, concrete or patio bricks. Basically, the foundation/floor needs to be protected from water damage and pests, both of which will come in from below and ruin a good coop.
Some screened windows or plain vents will help with airflow and humidity control. Dry bedding isn't so stinky and lasts a lot longer, so ventilation is key to everything from odor control, to preventing frostbite.
