I'm glad you're not wanting to keep more than 2-3 hens in there. Keep in mind that bigger is always better when it comes to keeping chickens, and we tend to end up with more chickens than we anticipate.
I started out wanting 3-4 hens in a cute 4'x8' coop. We now have two coops of that size in addition to a 24'x36' barn coop to house our 32 chickens. *wry smile* Just something to keep in mind: chickens can be addictive!
With that out of the way, I think an outside nesting box is a great idea. You only need one nesting box for every 4-5 hens, so more than one on a coop that size would be superfluous. I'd add a perch made out of a 2x4 with a poop board underneath it, to help keep the floor clean and lessen the chance of problems with cocci.
Personally, I'd go with a slanted metal roof with the slant toward the back. It might seem like an obvious thing to recommend but just this weekend I met some folks who unthinkingly built their coop with the slant toward the front so their run was a muddy mess! It's nice if the rain runs off the back!
I also think raising the roof and adding cross ventilation are great ideas. If it gets windy, you'll want a hood or something to deflect the wind coming through the vents, especially in winter.
Also, if it falls below 20 degrees or so in the winter, depending on the type of birds you'll be keeping, you'll want to orient the coop so that you have access to electricity and can run a heat lamp in there since adding insulation will probably take away too much space.
Have you thought about creating a small, attached run, maybe 2" high or so, and adding wheels to the coop so you can use it as a chicken tractor? It's a great way to fertilize the land, make sure your chickens have fresh ground to scratch, and keep them safe from predators.
Those are my thoughts, for what they're worth.
I hope you post the finished product!