For the second week I would suggest splitting your lodging between a town like Avignon and a smaller place like Saint Rémy because Aix-en-Provence is slightly away from most of the sites on your itinerary. Either way here is a suggested itinerary:
You could spend the first day exploring Bonnieux in the morning and then Aix-en-Provence and its fountains in the afternoon. Visit Paul Cézanne’s atelier and go to a nearby vineyard if you are interested (although you might get many more opportunities to visit vineyards on your way back to Geneva: http://www.chateau-la-coste.com/visit-us/ If you are going to do this then I suggest driving in order to access Bonnieux more easily.
You could spend this day visiting Avignon. The city is best known for its bridge (photo below) and the Pope’s palace. You could do an afternoon visit to Chateauneuf-du-Pape to taste some of the best red wine of the Cotes-du-Rhone region.
Days 3 and 4
You could spend the morning in Arles visiting the Van Gogh museum and cafés. From Avignon to Arles it is possible to take the train, but if you drive or find a minibus tour you might want to consider visiting Arles and the Camargue national park not far from here. It is a wetland where rice is grown and is known for flamingos (photo of a flock in the national park, below) and wild horses.
If you prefer splitting days into driving and taking the train you could club Arles and Nimes into a one day trip using the train, move to Saint Rémy the next day and visit Les Baux-de-Provence (15-20 minutes from St. Rémy by car) and the Camargue in a single day by car. Explore the narrow streets of the hilltop village of Les Baux with great views over the region. There is an old fortress that you could visit as well.
The reason I put Arles and the Camargue together is that Arles is like the gateway to this wetland. If you decide to club Arles and Nimes, in Nimes you can visit the Roman arena, the Maison Carrée (Roman temple) right in the centre of the city and the Jardin de la Fontaine (garden) with the Roman Temple of Diana and a little hillock with a Roman tower called the Tour Magne offering views of the city of Nimes. You could shift base to Saint Rémy de Provence on day 4. It might be a good idea to leave early and drive to the Camargue via Arles (around 2 hours), visit the area for a couple of hours and head to Les Baux-de-Provence for lunch and explore this little village in the afternoon before checking into Saint Rémy.
From Saint Rémy, drive to Uzès and visit Pont du Gard. This stunning, well-preserved Roman aqueduct was built to carry water to Nimes. I would suggest carrying some food and wine and having a little picnic by the river in typical French style – baguette, cheese, salad and pastry!
You could also visit the Haribo sweet and candy museum and factory in Uzès. Drive back to Saint Saint Rémy and visit the Roman oppidum of Glanum in the afternoon or do this on the next day.
Today you could visit Orange with its Roman Triumphal Arch and Vaison-la-Romaine. You can visit them both in any order stopping in one place for lunch. Vaison-la-Romaine has a Roman area along with an ancient bridge and a hilltop village. Return to Saint Rémy in the evening.
Since you would have covered all the main areas, you could drive to a couple more hilltop areas like Gordes or Saignon. Another option would be to add a day to your Saint Raphael leg and do everything as we had planned originally (without hurrying the Nice/Antibes/Eze part) and visiting the Verdon gorge as well and cutting a day off of this second week. What do you think?
The drive from Saint Rémy to Annecy is around 4-5 hours long and most of it along the Cotes du Rhones vineyards so you could see some of the harvesting and do some tasting along the way. Obviously, since you’ll be driving that wouldn’t mean much tasting! If you do visit Annecy it would be nice to walk through the gorgeous old town and take a dip in the lake.
A map the areas that you are part of the itinerary above,