I really like your branchline plan. The main part of the layout does get a lot track into the space.
How old is your son? He may develop an interest in operation soon too and forget about continuous looping. My grandson is 13 and has evolved in the last few years from having an interest in operating my continous run Lionel layout with a few routes and remote swtiches. Now he wants to run/operate trains on my 2 rail layout which is point to point and totally focused on operations. The operations have a through freight in each direction (from staging) which deliver/pickup cars at a yard. Then 4 local freights move cars to and from the yard to industries on the layout. This is all done with an automated car routing system that generates switchlists. The point is once my grandson started running one of the locals and figuring out where and how to switch the cars, he likes doing that now and ignores the opportunity for continous running.
My recommendation is make getting the branchline trackage in a priority. And from the style of that trackage, I think you could use manual switches since it is "walk-around:.
My son is 13 as well. Ironically, I was cleaning out the basement with him in preparation of starting my new 2R layout when he started to get nostalgic about running his RailKing stuff from when he was little. I definitely plan on having him run ops with me, and I hope he gets hooked like your grandson has. I am in a bit of a pickle as I sold off most of my scale 3R equipment over the years. I will be using my 2R rolling stock and I might even convert some of my 2R engines to battery and RailPro so I can run them along with the 3R.
You nailed it... I plan on manual turnouts to keep it simple. I was thinking card card system but I'd be interested in seeing your system for generating switchlists. I am going to have to limit my locals to terminal style ops that go to and from interchanges or staging. P robably 6 - 40ft cars.
I've always said that I'd run anything my son wanted to - as long as we were running together. Here's my chance, even if I do have to shelf my plans for a few years.