This was easily the rainiest tour of the alps I have yet done. We only had 16 solid riding days, rode 1501km, and had 33047m of climbing. We had 4 flats (one of which was self-induced), and one shredded tire. By far the worst damage was done by the airline, losing all of Mike's baggage. This tour is also likely to be my last alps-specific tour for a while, since at this point I've explored most of the places in the alps I want to explore.
Having done so, I can say a few definitive things: of the countries, Switzerland is easily the prettiest, while parts of France come a close second. Italy is a third. If you have limited time and can only explore one country in detail, I would say damn the costs and spend all your time in Switzerland. It is that pretty. The ride up to Melchsee-Frutt, for instance, as well as Grosse Scheidegg easily topped everyone's list here on this trip (and we have 2 members of the party who did not ride Klausen pass or Sustens pass), and it is for good reason Jobst starts each tour with these rides for many years. But be prepared for incredibly rugged riding! Switzerland is not for flat-landers if you want to truly appreciate the beauty of the country. Nevertheless, the general competence of the Swiss driver, the cleanliness of the country, the fact that most folks you run into will speak English makes Switzerland a pleasant country for the cycle-tourist. We have found very cheap places in the past as well, in B&Bs that are situated far enough away from public transportation that backpackers cannot drive up prices.
Lots of people will tell you that Italy has great food. Don't take that at face value. If you know where to eat in Switzerland, Switzerland is at least as good, if not better. Rosenlaui and Lammi, for instance, easily top all but the best place we ate in Italy (Hotel Gran Baita), and even that might be disputed. The French alps does have better food, but not by a lot more than Switzerland.
Before this tour, I was mystified as to why anyone would do an Italy specific tour. Now I admit that there is some justification: get an Italian out of a car, and he or she is one of the warmest, generous people you will have the pleasure of meeting. The country is cheap, and quite pretty. Bike paths through the valleys make riding tolerable, if you can find them and they go where they want to go. Having said that, Italian drivers were only well behaved on narrow mountain roads, and all too often take a "leave no prisoners" approach to driving that is only all too frequently seen in the USA. And if you were to count the number of "don't kill yourself on a motorcycle" signs on mountain passes (which are paid for my families of the deceased, usually), it seems that crashes occur on a frequent basis in the Italian alps. In any case, even after this trip, which has changed my opinion of Italy from a touring point of view, I still think that your efforts will be rewarded better in Switzerland or Austria.
Austria is the one country that I have not explored thoroughly yet, and it seems that I will have to do so one of these days. It is cheap, has great engineering in its roads, and excellent drivers. But for now, I think the Pyrenees are calling...