NavyChief, you gave me a chuckle.
My husband and I cruise Europe almost every year and have for over a decade, and I like the shoulder season a lot. We usually do a pre- and post-cruise stay in a couple of cities, and the crowds are smaller at all the sights in shoulder season as well as the advantage of milder temperatures and lower prices (cruises and hotels).
However, I agree with another post above that you should be prepared for anything. We have cruised in the fall with no problems, but we had a pretty dramatic weather pattern when we cruised from Istanbul to Rome about 4 years ago. While we were enjoying a nice port day in St. Tropez, which was a tender port, a fierce storm kicked up at sea, and the cruise line had a really hard time getting everyone back on board safely. In fact, one of the tenders ripped the stairs off the side of the ship, and we were all very thankful that no one was on the stairs. We were in the tenders trying to get back on the ship in 12-15 foot swells, which felt like it would turn the tenders over. The captain also had to skip our port the next day, Portfino, because it was a tender port too (my husband and I had already been to Portofino but others were very disappointed but understood due to the obvious weather situation). I must say that we were very impressed with the Princess crew.
On our last cruise in May of this year on the Holland Noordam, there were rough seas due to storms at night, but the Holland captain handled it as well as he could and altered our schedule a little accordingly. We called at the port of Marseille instead of Sete. That wasn't an issue for us because they were both in the Provence region, but some of the passengers had plans to go to Carcassonne that day, and that was not possible from Marseille. My husband and I are good sailors and don't get seasick but many on our ship did, so if you have a tendency toward that, you might have a higher chance of rough seas in shoulder season. Otherwise, I guess the point is that the weather is always a crapshoot, so my husband and I make our plans and then deal with any adversity that arises during the trip. To be honest, weather's a lot easier to deal with than the raw sewage in our cabin and other issues that arose during our cruise on the Norwegian Dream last year (that ship is a dump, and I do not recommend it to anyone), but that's another thread entirely.
Generally, it does tend to be more rainy in many cities in Europe in the fall. In Venice, there are problems with flooding that are being addressed with a major construction project at this time. Raised walkways are needed frequently during the spring and fall, and it is my understanding that this is more pronounced during the full moon. My husbaqnd and I have learned to make the most of what we're given wherever we are, and we've been very fortunate but do have some pictures of us in some lovely squares under our umbrellas.
So my recommendation would be that if the price is right and you like the itinerary, go for it and have some back-up plans.
Hope you have a great trip,