Where to stay 2 nights in Catania and 1 night Siracusa mid-March 2016?

I can only help you with a hotel suggestion in Siracusa, B&B La Via della Giudecca, Vicoli III alla Giudecca 4. Short walk to the Duomo and in the historic center of Ortigia, with a great daily market.

I have visited Mount Etna from Taormina, which I much prefer to Catania. You can get information on transportation to Mount Etna from your hotel in Taormina if you decide to stay there. I don't know about public transportation to get to the base of Mount Etna, but there are tours, and once you do get there, if you want to get near the top, you can take a 4-wheel drive ride further up. There is also a funivia but I'm not sure how far up it goes.

If you fly out of Catania, you will have plenty of time to gaze at Mount Etna over a cappuccino at the airport.

For Comiso, airline choices are limited (Ryanair is the only carrier to Rome). But for Catania to Rome you have multiple airline options. Be sure when comparing to include all baggage charges. Alitalia flies this route, and since they include one check bag and probably have a more generous carryon allowance (you can carry a bag on Alitalia that you may have to check on some others), they may end up cheaper.

To learn about all the options, look at Skyscanner: http://www.skyscanner.com/

To get Alitalia's best prices on this route, use their International website, which has an English option. The Italian website has the same prices but is in Italian only, and the US website often shows higher prices for the exact same flights.

I didn't get to Catania, but Taormina is magic - I'd definitely stay there. There are many companies doing excursions from Taormina to Mt. Etna, but it's only worth going if the weather cooperates (when I was there, it didn't). As Zoe said, you can only get so far up on your own (even with your own car), and have to take special vehicles the rest of the way.

Thank you both! I used SkyScanner to book a flight from CTA to FCO. I'll find out if Vueling is about the same experience as RyanAir. And Zoe, we booked in Siracusa at B&B La Via Giudecca--thank you!
We also booked a Etna and Wine tour with Etna Experience out of Catania. I'll let you know how that was when I return.

@Zoe, we loved the B&B La Via della Giudecca, Vicoli III alla Giudecca 4, in Ortigia. It was charming, comfortable and convenient. We arrived during a thunderstorm and the host brought us a tray of tea and cake. Thanks for the recommendation!

So happy you enjoyed the B&B! The hosts are wonderful.