Walking the streets of Rabat is a great way of seeing the sights and the wonderful old houses with the enclosed balconies.
You need to be careful here though, as Cars and pedestrians share the same space and there isn't much room. I found that out when travelling on the Little Tourist Train. In some streets, the Train could only just fit! You can't walk on the footpaths, as cars are parked on them and on either side of the road, so TAKE CARE!
From Valetta,Sliema and other places in Malta you can book a halfdaytour in a minibus to Rabat, Mdina and Mostar for 6,50 euros p.p. In principle that is just a transfer to these places with a tiny bit of confusing infos in between by the driver, while driving.
They took me by a taxi from the hotel in Gzira (Hotel Milano Due) all the way to St.Pauls Bay in order to fetch 3 ladies from a hotel there and then the taxi drove us to Rabat and informed us that our bus will be there 45 minutes later and in between we should explore this place (he did not tell us where to go). I asked the driver whether we will be going to the Roman Villa as well, he said:NO (although it was on the list !). So instead of exploring Rabat I walked to the Roman Villa in order not to miss it. Then the tourbus came, a Ford Transit with 15 seats, all of them fully occupied and I had to sit in the front row with a lady and the driver.
We were driven to the entrance of Mdina (thats just about 5 min to walk) and we fixed another meetingtime after 45 min from Mdina.
So I walked back from Mdina to the catacombes of Rabat, because one of the ladies told me about that and I had seen Mdina already a day before by the hop-on-bus.
Finally we drove to Mostar before we were taken back to the hotels.
On this tour you have to choose between Mdina and the Roman Villa, both of them is not possible in the time given !
You could do this excursion as well on your own and stay at each place as long as you want to and you could take the public bus from Valetta, that is really very cheap.
Mdina and Rabat are at the same place and Mostar would even be in a walkingdistance of maybe 1/2 hour or a few min. by bus. The church stands out of the city, so you cannot miss it and the buses go there anyway.
Infos by the driver ? He did not even know the entrancefee for the Roman Villa and I had to correct him, when he said it is 7 euros (and the most expensive ticket was 6 euros), thats not really a big difference, BUT a tourguide really should know !