I was in both those cities just this past July. I'm in the process of writing up the trip report and hope to post it within the week. I agree that both Marseille and Dijon are wonderful so I don't think you can go wrong.
A day and a half is not much time. I had just a bit over that for Dijon (2 nights, about 48 hours) which I thought was good. Great size (the old town) - not so small you get bored in an hour, but small enough to easily cover the main areas. I felt it was the most "French" town I'd been in (I've been to France at least 10 times) - beautiful mix of architectural styles, center is mostly pedestrianized, some interesting (and different) museums.
Marseille is much larger but the area around the old port could easily be seen in your amount of time. It's a busy, chaotic city with lots of street art (e.g. really good graffiti) and a nice buzz. One advantage I see to picking Marseille over Dijon is that it sounds like the rest of your trip is all inland so being on the water for a day or two would be a plus for me. One highlight for me was the boat trip to the calanques. I did a half day one but if I remember correctly there were some that were only an hour or two so you could fit that it.
Here are my photos (I haven't labeled them yet but you'll get the idea) - https://andiamo.zenfolio.com/f667172952