Welcome. I agree with you completely. There are a lot of right ways to raise them. And there are often downsides to the different methods too. It is often a tradeoff. A lot of my suggestions or comments will not apply to certain type coops. Pick and choose as you will.
Don't forget to make the coop convenient to you, not just the chickens. If you are going to enter it, make it tall enough and roomy enough for you to work.
Determine how you will handle the poop. Some people clean daily. Some set it up to clean annually, especially with the deep litter method. Depending on you coop, make your roosts so you can get them out of the way to clean the poop, either removable or fold-up. If you plan to use a wheelbarrow, can it get through the door. Make the door sill high enough that the litter stays inside.
If you are building from scratch it will be easier, but try to set it up so you can do as much as possible without going in the coop or the run and stepping in the poop, like gathering eggs, feeding and watering, opening and closing the door to the run.
Doors should open out so the litter inside does not build up and block them. I'm converting an end of a shed into a coop. I'll have a door I can go from the coop to the run but a second door I can get into the coop without going through the run. I expect the run to be quite muddy at times.
Plan food storage. I'll use metal trash cans to try to keep the vermin out. Also plan where you will store litter and other necessities where they are convenient to you.
To try to keep the floor of the coop drier, I'll mound a few inches of dirt on the floor so it drains to the outside. Putting the coop on a slope where it will drain would accomplish the same thing. You might try trenching on the uphill side to keep the water out, but don't trench right at the coop. That could encourage predators to dig into your coop.
You don't want the roosts too near the nest boxes or over the food and water if you feed and water inside the coop. They poop a lot when roosting. And I saw a recent post where the chickens used the nest boxes to get to the roost and one chicken would stop off on the way up and roost in the nest box. Made a mess.
I plan on using 1/4" hardware cloth as the floor of my nesting boxes. I saw where someone thought they were more flexible and would reduce eggs breakings but I'm not sure I agree with that. The reason I am doing it is that I think it will keep the nests cleaner.
I'll put a window on the north side to avoid direct sunlight but give me light when I am working in there without turning the lights on. Chickens cannot see well in the dark and if the coop is too dark, they might hesitate to go to roost.
If you can, position your coop and run where you can see it from the house. You and the 10 year old will love the antics of the chickens and you will be able to better see if something is going on or if doors are open that should not be.
Plan a chicken prison. This is to break up a broody hen or isolate a hen that is being cannibalized or needs isolation for some other reason.
Bigger is better. Crowding leads to cannibalism and you might want room to get more chickens later.
Read Patandchickens ventilation page. It should be required reading for anyone designing a coop.
https://www.backyardchickens.com/web/viewblog.php?id=1642-VENTILATION
These are some of my thoughts and considerations. Pick and choose as you wish and as fits your situation. I'm sure there are people on this site that will disagree with some of this. I don't agree with everything I read here either. But I'm learning a lot and most of what I read makes good sense.
