Why don't you look at what there is to do/see in each city, then decide which ones interest you two the most. Just because I might think Naples is the best destination in the world (I don't - I have never been there), after you compare things to do/see in Naples and Venice, you might want to skip Naples and go to Venice instead. I think you get my point.

Remember too, if you spend two nights in any one city, you really only have one full day to see the city. You only have part of the first day and part of the third day, and people tend to not use their time wisely on arrival/departure days. Generally, I recommend staying at least 3 nights in any one place so you have two full days to see and do things.

Are your airline tickets already purchased? To avoid backtracking, is there any way to fly into Geneva and out of some city in Italy? Then no need to return from Italy back to Geneva. That will save you at least a day travel time when all is said and done.