The Musee Beau Arts in Lyon is fantastic; I thought that was the best thing I saw in the city. Lyon also hosts one of the best flea markets in France every Saturday. Your friend probably already knows this.
What I would do, with an eye towards history and art, is go to Nancy. There you have the birthplace of the Jugendstil / Art Deco movement, fantastic architecture, and one of the best places for students in their 20's to hang out. the University is huge and you'll find a lot of people your age to connect with. Galle and Daum still have art glass shops open, there's dozens of art galleries and shops, the indoor market is one of my favorite places to shop for regional specialties, and you can't walk a block without seeing a building worth stopping to look at. You can walk, but if you want something faster buy a used bike and join the crowds on wheels. (You can get one for 40 euro behind Basilica of Saint Epvre.) The Grand Rue is jammed with excellent shops, places to eat, used bookstores, and it's one of my favorite places just to sit and people watch. The Parc de la Pépinière is an excellent place to picnic, the Aquarium is unexpected, Palace Stanislaus is one of the worlds greatest public squares, and the art museum (across the square from the tourist office) is world class. Nancy was a huge strategic city in WWII, and you can see some of that if you look. Patton spent over a month trying to take it, finally winning by surrounding the city. (This is the city everyone is striving for in the old war movie Kelly's Hero's.) Spend 3-4 days here.
Then take a short train ride to Metz, another city often overlooked by Americans, but very pretty, and historically important. It also has one of the best cathedrals, with stained glass windows by Chagall, you'll see. The center of the old town, built around the church, is mostly military and gov't buildings dating back 400+ years. (The tourist office is in the old Armory.) Again the indoor market is excellent, but it gets even better on Saturdays when the whole area outside becomes a really good outdoor market. Metz was one of the most important cities in Rome until around 400 ad. It had a huge aqueduct, and large population. The Museum of La Cour d'Or (which is free) is one of the best museums in Europe, and has a fantastic collection of Roman artifacts, many of which are unlike anything you'll see outside of Rome. They have the best collection of lead coffins on display anywhere. You can easily walk around the old fortifications of the city, which are hundreds of feet high and now house some very pretty gardens. The modern art museum is interesting, the old town is picturesque, and you're only a short train ride to Paris from here. (Another short ride from Metz is the Museum of the Annexation, War of 1870, where Germany beat France, took over the Alsace - Lorraine, and became a country as we know it.) Metz was also heavily fought over in both World Wars, and you can see monuments to this as you walk around.