I think this could be an opportunity to add another layer of depth to FE. I would love to see two ships able to battle it out. On the ships colliding event, the two armies could be sent to a special tactical map which I imagine as appearing like the deck of the two ships, with a few places to cross between them. After combat was resolved, whoever won would get control of both ships. The units that crossed over to the other ship during tactical combat would be on board the captured enemy ship, the rest of the garrison would remain behind on the original ship. Not sure how heroes that fell during the battle should be handled. I would say it makes the most sense for them to remain behind on the original ship if their side won, or warp back to town if they lost.
Once the code for Ship/Transport behavior is fully fleshed out, I can see some cool potential mod ideas. I would love to have the equivalent of magical flying fortresses or air ships with the air movement tag. Imagine sailing over a mountain range to strike terror deep into the heart of enemy territory, right were they felt most secure. Or what about magical "Drop pod" equivalents, transports that can make a one way trip into enemy territory. Those would be a great way to seize an enemy's crucial resources or get a much needed foothold in their territory. What does everyone else think?