I was in Sicily from April 28 through May 8, 2014. I went with my friend Eric, who lives in Philadelphia; we have each been to Italy multiple times before (separately, and four times together), but never to Sicily. I'm posting this in pieces, so if any one has any questions that I can help with and haven't addressed yet, please ask.
First, the itinerary:
April 27: Train from NYC to Philadelphia; fly US Airways from PHL to FCO
April 28: Fly Alitalia from FCO to Palermo
April 29 Palermo
April 30: Pick up car, drive to Monreale, then to agriturismo near Caltanisetta
May 1: Agrigento; overnight agriturismo
May 2: Villa Romana, drive to Siracusa
May 3: Siracusa
May 4: Ragusa and Noto; overnight Siracusa
May 5: Taormina
May 6: Taormina
May 7: Drive to Catania airport and return car; fly to Rome and stay in Rome Airport Hilton
May 8: Fly Alitalia FCO to PHL
The flights were determined by several factors. There are no nonstops at this time of year to Sicily from anywhere in the US, and the flights are expensive. Eric had already gotten a mileage ticket from PHL to FCO, and it turned out it was half the miles to do this vs. using miles from NYC to FCO. And the mileage tickets from NYC all the way to Sicily had convoluted routings. So, I took the Amtrak train from New York and we met in the PHL airport. I wouldn't recommend this unless you are familiar with the process, but I take that train all the time and know the stations well (including locations of elevators), so it was easy. Of course, the train wasn't free ($39 from NYC to PHL and $53 from PHL to NYC).
Next, we bought separate tickets from FCO to PMO, and from CTA to FCO. We were aware of the pitfalls of this, so we had to stay in Rome the night before our flight back to the US. Also, we had a bit less than 3 hours to change planes in FCO on the way in, and we were worried about this. We ended up buying two tickets from FCO to PMO; one with the 3 hour connection, and one 7 hours later, just in case. Each ticket was about €75, so I just figured the cost of our Rome to Palermo segment as €150 and accepted that. In the end, we made the connection with plenty of time. Alitalia didn't charge extra for our checked bags (Easyjet and Ryanair would have).
I don't regret doing all this, as I did save a lot of money. Flights with a decent schedule from NYC to PMO and CTA to NYC were going to cost about $1330. My mileage ticket had fees of $64, my flights between Rome and Sicily were €210, and my trains between New York and Philadelphia were $92 (so grand total roughly $450, plus 55,000 miles).