Been there. Done that. The train arrived very early to go across the water. All trains have to go across the Straights of Messina some way. Depending on the time of year, it may be dark when it happens.
We went from Rome to Catania on a night train. We did arrive sleep-deprived and exhausted. I'd never do it again.
If you must take a train, do it in the daytime when you can see something along the way. There are options that leave early in the morning and arrive in the evening. Some have no changes, some have 1 or 2, but the hours on the train are about the same, 11 - 11.5. The overnight train is longer. You can find them all on Trenitalia.
To see the routes, use DB Bahn. With those results you can see the exact route on a map. Some seem to go right along the water. You can also see what time you arrive in Villa San Giovanni and Messina to see when you'd be crossing the Straights of Messina.
If you aren't up for a very long journey in spite of the scenery, fly.