I haven't been to Italy over the Easter period, but it's a popular time for folks to travel when they want to avoid high heat and peak-season crowds. Therefore, the most popular cities will be heavily trafficked (affecting hotel rates), and you must be aware of the need to grab your key sightseeing tickets early. The two that immediately come to mind are the Colosseum and Vatican Museums in Rome, but there will be an issue or two in Florence as well, I assume.
I consider 2 nights in Venice inadequate, especially when it's your landing point in Europe. You may be sleep-walking zombies on your arrival day, leaving just one real day to explore Venice. That's a problem, because it most likely means you'll spend a great percentage of your time around the San Marco and Rialto areas along with all the day-trippers who what to see those same sights. (Have you seen photos of what small port towns look like whan a large cruise dip arrives?) You need time to wander around the back streets in Venice to appreciate its charm--maybe hop on a vaporetto over to Burano, just as one example.
Three nights in Rome is also a very short visit.
I think with 13 nights (12 days) you're spreading yourselves awfully thin by trying to travel from Venice all the way to the Amalfi Coast. I love Venice, but I'd tend to drop it this time so you have more time for your other stops.
I agree that your outbound transportation options will be better if you travel from Florence to Naples/Amalfi Coast and then to Rome. Otherwise, your last full day in Italy is likely to require relocation back to Rome for your flight departure.