Bob, no matter how you slice it, you're going to have to compromise on the view. Your height actually has little to do with it because no matter how short or tall, you still have 12" to 18" between levels to deal with. Your eye level is going the be around 60". If you start with the main level at 40", the upper level will be between 52" and 58". But that doesn't count the height of the trains that are about 4.5" tall, so you're really talking 56.5" to 62.5".
IMHO, anything over 15" is too high, especially when the train is going through the reversing loops. Otherwise the train will be along the wall, so being able to see over it is a moot point. And, when it comes to the loops, I'm not sure that's a big deal either. Looking at my latest design, I changed the location of the siding in the bottom loop. I'd run through it by taking the 1st turnout to go around the loop, stop past the 2nd turnout and back up to service the siding. that way even at 55", you'll be able to watch the action.
And when it comes to the view, I changed the location of the lower right crossover so the turnouts weren't covered by the upper level decking. I added a siding in the upper right off the blue main to make use of that space below the upper level. I relocated the siding beneath the upper level loop and added a passing siding along the yellow run so the siding could be serviced without blocking the yellow main. There are 3 turnouts covered by the upper decking, but if you place the landscaping on a pop-out section, you'll be able to access them fairly easily. I added a few more buildings too, but didn't have the ones shown in your drawing. If you'll send me the basic measurements for length, width and height, I can create some objects to better show placement. Oh, and I a.dded a river, but only on the upper level
