I haven't taken the tour but have skimmed through the itinerary. To me, the biggest omission is the Baroque towns SW of Siracusa--Ragusa, Noto, Modica and Scicli. So that's the direction I'd head at the beginning--but be very careful about driving jetlagged. You probably won't be able to accompish much of anything on your arrival day, so I'd expect to be visiting the little towns (whatever you have time for--I'd rank Ragusa #1 for sure) on Day 2.
Then at some point that day I'd head toward the northern coast, cutting through the interior, perhaps stopping briefly in Caltagirone and/or Enna. Perhaps someone who has actually taken the tour in its current configuration can say whether you will see any of the town of Piazza Armerina before or after your visit to the Villa Romana del Casale. Piazza Armerina seemed quite attractive through the window of my taxi. I'm sure there are lodgings in all of those towns if you don't want to drive all the way north on Day 2.
Cefalu is worth a stop. A few hours were enough for me (not interested in beaches or shops selling beach gear), but some others are bigger fans. So I'd try for brief visit there either on the evening of Day 2 or on Day 3 before heading to Palermo. You'll need time to drop the car. Do not attempt to drive in Palermo!
I think what I've laid out is too much for the time you have available. I'd certainly want more time to accomplish it. But perhaps this will give you some ideas.
If you go to ViaMichelin.com and zoom in on a map of Sicily, you'll see the most scenic roads marked in green. One mostly-green route runs from Caltagirone through Piazza Armerina, Enna, Leonforte, Nicosia and Mistretta to the coast, where you'd turn west for Cefalu and Palermo.
Palermo deserves more time than you'll have there during your tour. It has museums and many lovely churches and chapels.
