I will go against some conventional thinking here and say that IF you have a very large run (with at least part of it covered) and IF you let them out into the run very early each morning, and IF you have plenty of roosting pole length, then your coop will be fine for 12 birds. It'll be snug, but in my experience, the chickens are never ALL in the coop except for when they roost at night. Then they're on the roosts and not moving around the coop. You can also make more room inside your coop by putting in a platform. That gives the chickens space on top and underneath it. Having a large run is important because that's where they'll be except for when they're roosting or laying.
When you build your run, you can put hardware cloth all around the bottom of the coop so that chickens can go underneath the coop - which automatically gives them more room in the run, too. You can't see it in the photo I posted above, but the area under our coop is open to the chickens. We have hardware cloth attached to boards, and then the hardware cloth extends out from the coop also to prevent predators from digging under. We covered the hardware cloth with dirt and then landscaped around it so it isn't noticeable.
And yea - that's more nesting boxes than you'll need, but there's probably not much you can do about that. Once you get it, though, you might be able to remove or convert half the nest boxes to give more space for your chickens inside the coop.
Good luck!
