I personally don't like eliminating the yard track and the ready track. I also like run-arounds in towns, not necessarily long enough to be a passing track, just enough room to run around 2-3 cars while switching. I like the branch like a lot. I don't car for the 3rd inside loop. I guess if your goal is to just loop 3 trains, it makes sense, but if you want to add some operation, I think you could use the space better to add operating interest.
My favorite concept is 2-3 staging tracks - hidden or not - that can hold complete trains. Then a single track main with passing sidings in each town. I would have "through" trains come in from staging to the yard, set out cars, pick up cars, and perhaps change locos and cabooses if it is a division point. then the through continues on and goes back into staging after a few loops or so. I would have one it each direction representing through traffic.
Then I would have a "crew" get a loco (older and smaller like switcher or geep) and make up a local train with the cars that arrived and take it to one or both towns. And maybe a second local for the other town, and one for the branch.
Basic switching at industries - car type for car type - if you pickup a boxcar, you set out a boxcar etc. No paperwork. If you want some basic paperwork, make car cards for each car with a pocket for a way bill. Micro mark sells these or yuo can make them. then make waybills for each car type, boxcar, hopper etc. On one side place an industry name that uses that car type. On the other side place one of the staging tracks (Interchange or other RR). When a car is on the staging tracks. put a new waybill in the pocket routing it to an industry. When at the industry, flip the waybill routing the car to one of the staging tracks/through trains. It is a pretty simple system to set up.