We stayed just outside Rabat and love being able to walk into the town and then through to Mdina. We will return to the same place as it suited us very well. You have to visit some of the catacombs, though I must admit I struggled with claustrophobia there. Can I suggest you read The Kapillan of Malta by Nicholas Monserrat before your visit, if you haven't already, of course?
All quite busy around St Julians and Sliema, but some lovely places on the west and south west coast: quieter and prettier. Somewhere down that coast line was a prehistoric village which was very well maintained and well worth a visit, also The Blue Lagoon nearby. An intriguing place to visit, if you can find it as its well hidden, are the prehistoric cart tracks. They're near Dingli cliffs and a complete mystery.
The roads will be busier than VG of course, and lots of roundabouts and traffic lights if my memory serves me rightly.
Just thinking about Malta makes me eager to return. And the people were so friendly too!