Fortunately, jet lag shouldn't be problem. We will be arriving from the U.S. in Barcelona, where our daughter and son-in-law live, and we usually spend a few days there to get over jet lag before moving on. At the end of the trip we will fly back to Barcelona from Marseilles or Lyon, depending upon where our home base ends up being in the southern Rhone Valley. I was thinking to fly back from Avignon, but there are no direct flights to BCN and it looks like more of a hassle.
About Paris... there are a couple of reasons to keep Paris down to three days (actually 3-1/2 days). The first is that 3 of us have been there before and that we all agree it will not be the last trip, so we needn't see it all on this trip. The second reason is, quite frankly, budgetary. We are trying to achieve certain aims with lesser costs. We are traveling with our daughter and son-in-law and they want to share costs, but they need to keep them down to the extent possible with such a trip as this (our Portuguese trip was really cheap by comparison). So in Lyon, we hope to have great meals but not quite at Paris costs, and in the Rhone Valley, really good red wines will be more affordable than in Bordeaux or Burgundy. Wines are an important part of our trip, so we do not want to short-change them, and we look forward to tours and tastings while we're in the valley.
Also, right now we really only have a day and a half in Lyon, because of the day trip to Perouges, which sounds really fun and a bit different. So Lyon is already absorbing half of our travel day from Paris, and we might skew it to even later in the day if we can store our luggage at the hotel in Paris until it is time for the train to Lyon. That would leave us with just one day and two nights in Lyon, which would be OK.
We will definitely stop by Orange for the Roman ruins on the drive from Lyon to the Rhone Valley. I have not been to Rome, although the other three have, and I would really like to see the ruins. They sound wonderful!