We have stops on our cruise in both Messina and Catania ports. We can tour Mt. Etna and Taormina from either port. My question is which area has more to do and we’ll schedule Mt. Etna/Taormina for the other one. Sorry, I’m not familiar with either.
I guess what I would want to know is what would your other options be from those ports? My first thought is that from Catania you are closer to Siracusa/ Ortigia, which is very worth seeing, so I would probably do Mount Etna and Taormina from Messina.
I would say as well though, that as much as I liked Taormina, we stayed overnight, and it did get very crowded in the mid day and became less charming.
I think there's more to see and do in Catania (even aside from exploring the possibility of heading out of town to Siracusa)--the WWII Museum, the market and the pretty historic area around the Duomo.
However, I'd consider the cost of the cruise-line excursions (if that's your plan) and/or transportation schedules if you're considering the do-it-yourself approach.