Hi Noir18 -
I've travelled a lot in Switzerland, and have never used a guided tour. I'm sure I've missed something that way.
Arno has given you some good ideas for a foundation for your trip, and you've picked places that are definitely worth visiting. Luzern is a lot more scenic itself, and has a greater range of activities for a first time tourist than does Zürich. By the way, they are only 45 minutes or so apart by train.
along with a good zoomable map -
Also, you'll have a reasonably late sunset at the end of August. Sunrise at about 0640; sunset at around 2010.
I do have some thoughts about your question:
<<"They are quite similar and I was wondering if it would be better to swap one of them to Glacier Express. Is there a train going over Alps to Milan -my next stop after Zurich. And that doesn't take too many tunnels?">>
In addition to the actual destinations, train travel in Switzerland offers a lot of wonderful scenery along most of the routes. Often, the trip is nearly as interesting as the destination. The traditional trans-Alpine trains are among the most scenic - you have noted the Glacier Express which travels through and over the Alps, and can get you to Milano via a circuitous route through St. Moritz/Pontresina/Tirano/Lugano.. By the nature of railroads through the mountains, there are a lot of tunnels on any route, including many short ones on the Albula Pass section of the Glacier Express, for example.. Most are short. In contrast, the newest and fastest trans-Alpine routes use long tunnels, newly dug at lower levels than the old ones. Open for tests this coming summer, and for passenger traffic this coming December, the tunnel under the Gotthard Pass will be 57 km long, and, if I recall correctly take about an hour off of the journey to Milano. It also removes the scenery on the best portion of the current route.
Tunnels don't offer the most beautiful scenery as you surely have recognized. ;-)
One of the most scenic rail routes in Switzerland is the current route over the Gotthard Pass, beginning at the southern end of Lake Lucerne, at Flüelen, and continuing to Milano via Bellinzona and Lugano. Many people, including myself, make a special effort to ride that train, and we have been relieved to learn that the route will be kept open after the new "basis" tunnel opens.
Since it is easily accessible from Luzern (or Zürich) , it is definitely worthwhile, and the Wilhelm Tell Express mentioned by Arno adds the beautiful boat trip on Lake Lucerne.
I'm not sure what route you could fly into Milano. if it is to Malpensa, you have a significant train or bus ride into Milano from the airport. Linate is closer, offers many intra-Europe destinations/connections, but does not seem to offer flights to/fromSwitzerland:
A second trans-Alpine route, also with a boring new tunnel is now in use, while the older, higher scenic route offers magnificent scenery. It is from Spiez, near Interlaken, up and over the Lötschberg Pass via Kandersteg, and down the side wall of the Rhone Valley to Brig, thence to Italy at Domodossola and onward to Milano.
The new tunnel runs under the most scenic part of the first leg, from near Spiez to Brig.
Luckily, the scenic old route as far as Brig is served admirably with hourly service on the "Lötschberger" train.
That route is less obvious from Luzern, but if you did wish to use it from Luzern, an added first leg would be the extremely scenic Luzern-Interrlaken Express via Meiringen and the Brunig Pass to Luzern.
The point of these comments is not so much to direct you to any specific train route(Although the Gotthard Pass is worth the detour, as they say) , but rather, to alert you to the fact that the journey by train in Switzerland can be as nice as the destination.