Well...that's a hard one. Both are very rich in history and great architecture, Marseille having the added bonus of being on the frontier of a clash of cultures with a lot of North African immigrents arriving there.

Marseille has the sea, while Avignon has the river Rhône. Marseille is also considerably bigger. Avignon can probably be visited in a few hours, while Marseille would take considerably longer. Also there are many more things to see around Marseille (calanques,...) than around Avignon.

Still, not an easy one to resolve, I haven't been more than once or twice to both towns, so can't really help much more, any way it's easily possible to burn through a lot of SD cards in both...