I haven't gone out to the lavender fields myself, but I think you'll be too early to see the views you're probably anticipating. Google is telling me the fields begin to bloom around the end of June, and I think the peak period is in July. For future reference, I believe you would need a car to reach the lavender fields.
Avignon, Arles and Aix-en-Provence are all attractive places with things to see. However, if you spend just two nights in Provence after traveling there from Paris and want to devote one day of your stay to a day-trip to Marseille and one of the Calanques, you will not have much time left to see the town where you're staying, so perhaps travel time will be of as much importance to you as the specific characteristics of that town. Have you considered simply staying in Marseille?
There is some variation in travel time from one departure to the next; you can look at the schedules for your specific travel date on the [Deutsche Bahn][1] website), but these are reasonably accurate, relatively speaking:
Approximate one-way travel time from Paris by train:
Aix-en-Provence: 3 hours
Arles: 3.5 hours
Avignon: 2.75 hours.
Marseille: 3 hours
Approximate one-way travel time to Marseille-St. Charles:
Aix-en-Provence: 55 min.
Arles: 55 min.
Avignon: 35 min.
Marseille: 0 min.
Approximate one-way travel time to Nice-Ville:
Aix-en-Provence: 3 hr.
Arles: 4 hr.
Avignon: 3 hr. 40 min.
Marseille: 3 hr. 10 min.
It appears you'll spend somewhat more time on the train if you choose Arles as your intermediate stop rather than Avignon or Aix-en-Provence, but the fast trains to/from Avignon and Aix-en-Provence use separate TGV stations outside of town, whereas you don't have to go so far to reach the single Arles station, which is served only by regional trains (TERs).