Trains from Basel to Milan

I am not sure you can. Most of the trains will follow the same route. Personally don't think that trains are good for sightseeing since they tend to run in corridors often lined with trees and poles resulting in limited views of the country side.

There are 4 direct trains a day. 6:28, 12:28, and 17:28 are the fastest and go through Bern, Spiez, Brig, and Domodossola. It uses 2 "base" tunnels that go completely under the mountains and takes 4 hours and 12 minutes. The other, at 11:03, goes Luzern, Arth-Goldau, Lugano, Como. It uses the largest base tunnel in the world to go completely under the Alps and take 4 hours and 47 minutes. So neither of these provide great views of the Alps.

But if you want to take a bit more time and don't mind making a few train changes, there are ways to improve your views. You can take an older route mostly over the mountains by specifying "via Kandersteg" on the first route. Then you will change trains at Spiez and Brig and take an extra hour to get to Milan. You still have one base tunnel, the Simplon Tunnel into Italy, which was once upon a time the longest tunnel in the world.

Another route is to specify "via Goeschenen". Then you will change trains at Luzern and Erstfeld and use an older route that uses a shorter tunnel and goes mostly over the mountains. That way takes 6 hours.

The new, longer Gotthard tunnel has replaced for express service the old railway section between Erstfeld and Biasca, but there are plenty of scenic glimpses before and after the tunnel - for example the section around Lugano has a lot of lake views. The old section is still in service - it is the itinerary via Goschenen - it is in a nice alpine setting and has exceptional interest to the railway enthusiast, with spiral tunnels, a point where the line crosses two times over itself and the Wassen church that can be seen from three different heights. But as for dramatic mountain landscapes, you get only a few glimpses every now and then.