Yes, I agree that Aix is very worth a day; it's easy to walk around the central part of the town, and easy to reach by train from Marseille.
Marseille itself can be controversial, and about a year back, there was a discussion on this site covering pros and cons. For me, it was someplace to pass through until friends moved there, and then I gradually spent more time, and liked it more. There is certainly an interesting cultural mix, and some have even suggested that "it's not France". An easy tour would include vieux port, and possibly some bouillabaisse while there. There is also a metro system, which I used to travel to my friends' home when they lived there, but I can't really tell you where to go by metro, since I went only to a single destination.