Your schedule is too convoluted to answer. You have mapped out a few itineraries and then you talk about spending time in Florence but not at museums without listing any plans to stay there. You cannot do a day trip to both Pisa and Florence and then spend the night in either Rome or Venice. You would need to spend a night in one of those cities from both a travel and enjoyment aspect. Also, I agree with the poster above. Why would you bypass both Florence and Pisa to go to Venice just to travel back south to those cities and back north to Switzerland? That’s a lot of time wasted. A much better schedule would be:
Rome-Pisa-Florence-Venice-Zurich/Geneva-Paris-Madrid
If it’s a coin toss between Geneva and Zurich, then it really depends on what you’re looking for. If you are asking which is the better city to visit, then it’s Geneva. Zurich is a lot like Frankfurt in that there are some decent sites, but it’s mostly a business/financial town. However, if you are taking a train to Paris, you will have to route through Zurich at some point regardless. So, from a pure travel aspect, Zurich makes the most sense if you only have 2 days. Those pesky Alps will play a factor in what you can see/do in the time you are allotting.
I’m assuming that you want to take a train from Venice to Switzerland for the scenery. Figure on about 8 hours between Venice and Zurich. It’s about 6 hours from Zurich to Paris on a day train. I would also fly between Paris and Madrid as a train will be 13+ hours and cost you more than an EasyJet flight from ORY-MAD. (Especially if you are taking children…ouch!) Sleeper cars are more cramped than a cabin on a cruise ship and it makes much more sense to do a night train on that leg as there isn’t really any scenery to speak of.
Lastly, this thread is probably more appropriate for the Europe forum as Italy is just a sample of the places you are looking to travel to.