Good plan! (I live in Switzerland...)
some of this has been said already, but maybe I can still add some infos... Depending on the duration of your trip you should do as much as possible by train. The system throughout Europe is great, and if you book in advance you can get good deals. Within Switzerland you can get a general ticket that is valid on all trains, as well as public transport in all cities. Most boats on the major lakes are also included or at least give you a discount if you have this ticket. As a tourist you can get it for a reasonable price (check
www.sbb.ch, the site of the national railway company). Special trains like the one up to the Jungfrau Joch are not included but might give you a discount.
For general travel in Europe the train is also good, but is often more expensive than flying. But it is way more relaxing and lets you see the gradual changes of landscape and people as you travel from Geneva to Munich and Prague.
I recommend you also go to Berlin. This really is a phenomenal city with A LOT to offer, whatever you desire.
Aside from the mountains in Switzerland you will find quite pretty, old medieval town centers; Zurich, Bern (there are several more in Switzerland since it did not get bombed in WWII), Prague, and Paris - there in particular the Marais - are nice. Munich is missing that to a large extent (for obvious reasons), but still has some nice corners. The English Garden is very nice, and around the Odeon and Marienplatz you will find pretty spots.
The lakes in Switzerland also offer a lot for photography. Lake of Zurich, lake of Lucerne (and Lucerne itself), lake of Geneva in particular. If you are in Zurich you should go up to the Üetliberg from where you will have a great view over the town and lake of Zurich. There is a small train going up, otherwise it is a very short hike.
In Berne, if the weather is good, go to the University (which is very central, near the train station). It is slightly higher than most of the rest of the city and gives you a spectacular view of the alps.
As a last tip - if you take the train from Bern to Geneva make sure you sit on the left side (looking in the direction the train is moving) and have a window seat (top floor if it is a double decker train). If the weather is good you will have a breathtaking view when the train reaches the lake.
I don't know how long you are planning on staying in Europe, but each of the places you mention deserve at least a couple of days, Paris probably a week (Berlin as well) at least...
And about the equipment - I tend to agree with what the others say... Even though I have, in fact, seen people with big white lenses (including myself
) I don't think there is a need for the 70-200 or any of the extenders. Wide is nice since there will be lots of opportunities for landscapes but you will not need much on the long end. And in the worst case there are rental places where you can just pick something up
) More looking for cautionary warnings and such, but any advice will be GREATLY appreciated. 
