As a general assessment. What you have is a massive yard and a few industries. The main point of the yard as I see it is to classify trains. With no staging, you will be limited in operational variety as to how the trains are classified. Your yard ceases to be a classification yard and becomes a defacto staging yard. My club has a yard like this and switching is limited to setting full trains in yard tracks for the next person to take on a loopty loop. It may not be that bad, but not much better either.
You have one passing siding near the yard and no run-arounds which means all of your industrial switching depends on your wye. Using your wye in this way, if you plan to use the size of trains that your passing siding would indicate, will tie up the main and prevent the running of more than one train, which is ultimately the purpose of the siding.
My questions at this point would be 1) What is the purpose of your railroad?; 2) How do you see it running?; and 3)What is the unifying theme that ties it all together?
Perhaps you've answered those questions already, I've forgotten.
I'm also wondering about the purpose of the auxiliary yards off the main double ended yard. First of all I wonder at their purpose, maybe some sort of deep storage for cars to be delivered at a later date? At any rate, a single switcher will have to jump through hoops to switch both sides. Unless that long track on the right side of the yard is your intended runaround. But that jambs up the main yard for switching. Sorta thinking and typing here. I like plans to make obvious sense. Maybe I'm missing it.