We will be in Beaune for 3 full days. Is an all day trip to Lyon worth the effort or should we just stay in the Beaune area?
I don't like Beaune as much as many others so I would take the easy day trip to Lyon, which is a much more interesting place, in my opinion. Three full days of Beaune would be two days too much for me unless I spent the days exploring the neighboring wine towns, countryside and Dijon.
I agree with JHK - besides, the food options in Lyon are much better, IMHO.
Lots of interesting history in Lyon, too.
I'd certainly make the day trip to Lyon. Actually, if it were me, I'd rather stay in Lyon and make a day trip to Beaune. There's so much to see and do (and eat) in Lyon.
I also agree that one day in Beaune is enough. Lyon has so much more to offer as to sights and restaurants that two days there is easily warranted.
Sorry to just "ditto" without adding anything, but I think you are getting good advice. One day is plenty in Beaune. You could spend a week in Lyon.
We just came back from 3 nights/2 full days in Beaune and had a wonderful time. The first day we went to the delightful Saturday open air market and toured the medieval charity hospital - Hôtel-Dieu. The second day we had so much fun renting bikes in town and riding south of Beaune through the vineyards and famous wine villages stopping along the way to taste wine and eat lunch. It seemed like the perfect amount of time for this beautiful town. As far as Lyon, we spent 4 nights/3 full days there last year and never ran out of things to see or do in this fabulous city. In my opinion, both are great travel destinations and your decision depends on if you want more time in a classic Bourguignon wine town or a charismatic French city.
Just to elaborate a little further: Lyon is 2 hours away. For me that is not a day trip. But it's a marvelous place.
Beaune can be a brilliant base to explore the region by car or bike. If that is what you plan, don't worry about being bored.
So I would say: Love the one you're with and explore Burgundy. On the other hand if Lyon is enroute to someplace else, such as Provence, you would not regret spending a night or two.