If you are into 20th century architecture, be sure to visit Le Corbusier's Cité Radieuse. There is also a restaurant in it, which is not that great, but the view is spectacular (the restaurant is called "le Ventre de l'Architecte").
Avoid restaurants on Le Vieux Port.
High street shopping is on Rue de la République and Rue Saint-Ferreol, chic shopping on Rue de Paradis, alternative shopping on Rue Sainte, antiques shops are behind the Prefecture.
Bars popular among locals are located around Cours Julien.
Visit Notre-Dame-de-la-Garde church, it is the highest point in the city, and a figure for locals, even if they are not catholic.
Marseille is beautiful in an intriguing way but not "pretty", it feels a bit dangerous, dirty and kinky you may or may not like it (it is the city in France with the highest rate of homicides). Many areas of the city centre will make you believe that you are somewhere in Morocco and some people may not feel comfortable with it.
Aix in much more consensual (pretty, clean, affluent), in fact Aix almost work as a posh suburb of Marseille.