Dijon or Lyon for a side trip from Paris?

Dijon is a lot smaller than Lyon and if you have only a couple of nights to spare it's far more manageable. Also, since Dijon is pocket-sized, easily walkable and packed with rustic charm it makes a fine contrast with the big-city glamour and dash of Paris.

Rather than putting Dijon in the middle of two bites at Paris, I'd be inclined to spend five nights in a single location in Paris, then travel to Dijon and return to Paris only for your flight out. Packing up and getting yourself to a different hotel or apartment is a tedious business that saps time and energy from the more appealing aspects of travel, such as lounging about in cafes. The Marais is a fine address but you pay a premium for staying in this chic and artsy quarter. Go just to the north to the Republique area and you'll pay less, with cool in abundance.