Swiss train Zurich to Milan - reserved seats? One ticket? Base tunnel route or not?

Can we choose a train that does not go through the Gotthard base tunnel but takes the longer more scenic route?

Yes you can. If you just put Zurich HB to Milano Centrale, you will be routed through the Gotthard Base Tunnel, because the SBB train planner always assumes you want the fastest, most direct route. To see the scenic route with the Treno Gottardo, you put in "Goeschenen" in the "via" box. you will then see the scenic route, you will have to change trains in Bellinzona back to the EC train to continue to Milano Centrale. By putting a way station along the scenic route in the "via" box, it will route you that way.

1. Some information says the system assigns your seat and once assigned, it cannot be changed. Some says just walk on and take the seat your want. Which is it? People recommend sitting on the left side of the train for best views. Do we just show up early and jump into the seats we want?

That depends on the train. If you book the direct EC service you will get a reservation included in your ticket.
If you book other trains (RE, IC etc...) it is indeed free seating. Showing up early just means you spend more time getting bored on the platform...

1. Is it just one ticket through to Milan, purchased on SBB? Or do we need a separate ticket for the Italian portion?

You can do this in one booking. If you book the through EC train you get one ticket. If you book the RE + IC/IR combination you will get two tickets. You can book on SBB or your can book on Trenitalia. If you book the direct train on Trenitalia you can pick your seats.

1. Can we choose a train that does not go through the Gotthard base tunnel but takes the longer more scenic route? How do I see that? The only thing I can guess is to take the train that takes an hour longer, but by route, it just looks like it is a local train with more stops, terminating at a different train station in Milan. I cannot see on SBB whether it does through the tunnel or not.

You can. But for that you will have to do your booking on SBB, you can't do this on Trenitalia. To get the mountain route add a "via" and enter "Göschenen". That forces the system to consider the route via the old line.

Thank you both for your detailed guidance. I really appreciate it. You are the best! Thanks, Ginny

One more question, is the scenic route worth the train change in Bellinzona? Thank you.

At least near term, if you take the 8:05 Treno Gottardo, you get off at Bellinzona on Track 3, wait 14 minutes, and the EC train to Milano Centrale arrives at Track 3, so you just get on board. Is it worth the train change and the extra 1 1/2 hours? You tell me.

Well, I won’t know unless I take both routes, which I cannot do on this trip. Have you taken both? Have a preference?

Neither. But last January I went from Zermatt to Luzern, a route I could have done in 3 1/2 hours, but since I had no reason to get there early, I took a scenic route that took almost twice as long. Do you have a pressing need to get to Milan early?

Can we choose a train that does not go through the Gotthard base tunnel but takes the longer more scenic route?

You asked the question, and I gave you an answer. The ball's in your court.