At MRS, stay airside—focus on food and rest as transport into the city is slow.
Skip the city for a layover under 5 hours. The shuttle bus takes 25 to 30 minutes on a good day, and traffic near the port can add 20 minutes to the return. A 3-hour layover does not leave enough margin.
Take the shuttle to Saint-Charles (EUR 10, 25 minutes). Walk 15 minutes downhill to the Vieux Port. Spend 45 minutes by the port and at the fish market if it's morning. Walk east 10 minutes to Le Panier, the oldest neighborhood in Marseille: narrow streets, good street art, and a few small galleries. Eat lunch at Chez Madie on Quai du Port: grilled fish for EUR 18 to 25.
With 10 hours, add the MuCEM (Museum of European and Mediterranean Civilisations) at the port entrance (EUR 11, 2 hours). The building bridges the Old Port and Fort Saint-Jean and is one of the best contemporary buildings in France. Alternatively, take metro line 2 from Vieux Port 20 minutes south to the Calanques National Park trailhead at Castellane for a 1.5-hour coastal walk.