What is the best way to get from Rome to Catania?
Last Sept I went by air. In spite of Al Italia's bad reputation I actually had two good experiences-the first from Rome to Catania and the 2nd from Palermo back to Rome. I was even brave enough to check luggage from Palermo to Rome and it arrived safely. I had thought about taking a train, but the short trip made me glad I opted for air and had more time to do other things than get from place to place.
You can also make that flight with a Rome-based airline called Blu-express.
Whichbudget.com is a great web site showing you the various lo-budget airlines that fly inter-EU.
They list Windjet, Blu-express, and Meridana/Eurofly as options for that route.
The train trip is quite long, but absolutely beautiful.(We have done th Naples to Messina train trip.)
I would definately recommend one of the lo cost airlines.
Have you considered taking a night train? If you sleep well on trains, it's a great way to combine saving the cost of a night in a hotel with having more daylight hours for sightseeing.
There are two direct night trains. One leaves Roma Termini at 21:20 and arrives at Catania Centrale at 08:31. The other leaves Roma Tiburtina at 23:28 and arrives at Catania Centrale at 09:57.