Reactions to Plan
My overall reaction is WOW! You've resisted the temptation to go overboard on track, so you'll have lots of room for nice scenery, with plenty of separation between towns to give the sense that your trains are actually going somewhere, and that big radius curve between St. Jean and Morris is gonna be a favorite spot for train watching. Also I did some switching in my head, and there's a nice mix of trailing and facing point turnouts to make operating a lot of fun.
A couple of tweak thoughts:
(1) Like most everyone else here, I hate the idea of a duckunder. Going under once during an operating session may not be a huge deal if you're young and agile, but think about building the layout. Long before you get to operations you're going to be going back and forth dozens of times each work session -- to fetch a forgotten tool, to grab more screws, to take a structure back and forth from the workbench as you detail it, go get a cup of coffee, etc., etc. Any simple mechanism (a lift-out section, a hinge up, a hinge-down) would make things a lot easier for you. For example, I've got a really simple removable bridge (a 60" 1x6 with a u-shaped shelf bracket track over each edge to prevent sag and a single track on it, plus a stereo plug to power the track on top) that just lifts up and stands on end except when I'm running trains, and it works fine. From reading all the comments and your reactions, it seems to me that you're resisting something pretty easy to do that a whole lot of us think is pretty important.
(2) Is there really no run-around in St. Jean? I don't know the prototype, so maybe there's a reason you haven't included one, but I think operations would be more fun if you just tied the siding that parallels the main back into the main at its other end.
(3) I'm with Lance in urging you to create as much vertical separation as possible between staging and the underside of the main deck. On our club layout (www.crmha.org), we have a helix down to a double ended 8 track staging yard, and I added an extra turn to the track plan to get the staging yard a full 8" below the main level. Now I wish I'd added yet another loop! The problem is that Mr. Murphy will take up residence in one of those middle tracks, and 8" is enough to get a 1:1 hand in there, but not enough to do much with it when you do; plus you can't really get your eyes high enough over the yard to get a good view of a middle track. Are you willing to drop the elevation a bit between St. Jean and Morris to increase your separation? Sooner or later, you'll be glad you did, and it sure looks to me that you have plenty of room to do so.
(4) My layout is also switching oriented, and I don't really need a continuous run to be happy. But when your Aunt Tilly, who doesn't know the BNML from beans and probably could care even less, comes to visit and you want to show off all your good work, you're going to want to just let a couple or three trains run loops while you talk to her and whoever came over with her. I'll also confess that I enjoy letting a train run slow loops every now and then while I stand back with my adult beverage and just watch. My layout room is much smaller than yours, so you don't "need" the continuous run option for visitors as much as I do, but it sure looks to me that you have a pretty easy way to add it -- just extend the staging lead around the corner, through the little room with the single branch line staging track in it (btw, you'll improve your operating potential if you add a turnout and make that 2 staging tracks), and tie it in at the lower left hand end of the line. If it really is as easy as that, you'll be glad you added a continuous run loop, even one where so much of the track will be hidden.
Good Luck, have fun,
Sandy
http://www.sandysacerr.com