If you choose Arles, you'll change trains at Nimes and could spend a couple of hours there to see the two big Roman sites. Arles is the town that I've visited most among these, and was happy that I did, both on my own and with our tours, and it has the best museums. Both Arles and Aix have great markets on Saturday and at least one other day per week.
Avignon, Aix, and Marseille are all served by one direct TGV train in the afternoon. I did not find Marseille too seedy during a brief day trip last year, but Rick's book indicates that it's not the best place for finding good-value hotel rooms (but you can look around), so I went with a better-value (single) room in Aix.
Car rental offices are easy enough to reach in any of these cities, though in Avignon most are by the TGV station instead of the central station.