I've only seen a few of Notch's products, but none of them have included anything cookie-cutter. They follow rules, like "If the walls are solid and there is a door, then a bed works here." but there are no pre-set shapes to speak of. Designing a ship is a bit more difficult than designing anything else though, as it ultimately must be done from a detached 3rd person view to really grasp what's happening, but I don't know. If you were building the ship purely from the inside without a reliable overview or strategic grid, it would certainly make some very unique designs. I imagine you would end up with something very similar to oldschool DF construction, where it works beautifully and amazingly as a fort, but once you toss it in a visualizer you end up with some strange shapes and unusual structures that couldn't be explained by conventional design, and only work in dwarven design. Like building a massive, grand dining room with an extremely low ceiling.
On the actual gameplay though, I'm looking forward to one specific instance. I'd like to rig a ship with computers all over, each set to react to events and transfer information. Then, I want the ship to be struck by an asteroid or an attack or something, and for the ship to react according to its programming, right itself, damage control, and all the beautiful micromanagement automation that I never get to see anywhere else.
Mainly, it needs sudden events. Minecraft is fun, and redstone is fun, and using mods that add logic gates is more fun, but ultimately nothing surprising happens in Minecraft and your solid castle walls will always be solid walls. DF throws goblins, building destroyers, and untrapable creatures at you randomly, and the fort's reaction tolerances are what ultimately counts. Similarly, a ship running smoothly will only be entertaining for so long. You need unexpected explosions to make the design really shine.