Personally I like the idea of making ships a move 1 unit. I think it would create more obvious crossing lanes and drop zones. For example, instead of having like 3 ships together in a single sea zone shucking across a long distance, you'd be more likely to see little logistics trains, maybe across 3 sea zones with 1 ship in each. Basically short shucks with fewer units ground units moving at a time.
It would make the whole amphibious deal a little easier to manage, and probably make fleets somewhat less vulnerable to the dragons, in large scale all-or-nothing engagements, since you'd be encouraged to spread your naval units out. Basically more targets and smaller battles, so everything doesn't hinge on like one big battle where you might get totally wiped.