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If I were to go with three separate structures, I'd have specific breeds (or pairs of breeds) assigned to each of them.    My plans for runs would be separate runs, one for each of the three coops, if I were to go with separate coops.    I really like the design of the structure that Ed (Intheswamp) proposed however, and I think it makes even more sense, especially in having individual runs for each of the three sections within the coop.    I want to make sure that if I've got groups of chickens of different ages (and I will) that I'm able to allow the youngest and smallest to hang out together, rather than getting thrown into a huge communal run with absolutely every other chicken.
By the way, regarding co-existing. . . I meant to say that I'm not going to keep each single breed completely segregated (as I originally considered) from every other breed for the duration of its life.    I'd at least pair them up with one (or possibly two) other breeds.   In the case of the design that Ed posted, I'd have 30 co-existing in one partition; 45 in another slightly larger one; and 30 in the last.   I'd keep the original footprint of that design (30' x 16'), but modify the partitions to measure 8' x 16', 12' x 16' and 8' x 16', with the 1st and 3rd holding two breeds and the 2nd holding three.
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Again, I'm now leaning in the same direction, having seen the basic plans for the partitioned, Open-Front chicken coop that Ed posted.    If I'd eventually need to put breeding cages in each of the three partitioned areas, so be it.   
The one thing that I wonder about in that design though are the swinging doors that appear to exist between each partitioned area.    That almost seems to defeat the purpose of having separate partitions.   Further, I can't help but think the number of chickens who'd end up decapitated trying to run through a swinging door at just the wrong time. . . . granted, it WOULD make culling easier 
Thanks for your input, Pat.
John