With a stopover in Switzerland, the Bernina railway or the Gotthard Panorama route suggested above are the best options, my preference being the Bernina railway.
But to answer the original question: if you don't stop for the night, then out of the two routes, my preference goes for the Paris-Geneva-Milan route (or the Paris-Lausanne-Milan which can be quicker, but I have never done Paris-Lausanne so I don't know if it is pretty).
There is some great landscape in the last hour or so before Geneva, as well as from Lausanne all the way toward the Simplon tunnel. I have never been beyond Visp so I don't know about the scenery on the Italian section.
It is, overall, more scenic than the direct Paris-Milan train.
On the contrary, Paris-Zürich is very, very dull, and Zürich-Milan is much less scenic since the opening of the Gotthard base tunnel (you are left with views of Lake Zug, glimpses of Lake Luzern, and not-so-dramatic views of Lake Lugano).