If you are interested in creating prototypical operations, I'd recommend you come up with a transportation plan for the route. There are a lot of good
resources at
http://www.opsig.org/ that will help you figure this out.
Once the overall plan for the route is understood, then you can define the functions needed in the yard, which will act as guidelines for how it should be structured.
If you don't care about prototype ops, then do whatever you want. Some will like it, most who value prototype ops will probably not be impressed.
I wonder why you would need all the crossovers. A properly managed yard does not store cars and then pull them as needed. It sorts cars as they arrive and put them into the next train that will be headed in the proper direction. So, each track in the yard represents a destination or group of destinations in a general area. As a train arrives, the cars in that train are sorted or "classified" by destination. Depending on you operation plan, an outbound train will be made up either at a specific time, or when a sufficient number of cars have been accumulated. There a books written on yard operations, so please don't think that this short explanation tell the whole story.
As for using AI, I have been quite successful creating a rather complex prototype yard, using AI to bring in all the inbound trains and also to take away the outbound trains. This yard has 26 classification tracks, three arrival tracks for southbound and three arrival tracks for northbound. It includes an engine facility with turntable and roundhouse. It also uses an AI driver to pick up the cabooses from the arrival tracks and store them on the caboose track.
Best of luck with your venture.
David