I love player-created content. But, of course, most players are not creating content with pro-level 3rd-party tools. They are creating content with whatever the in-game content tools are.
For example, you can create a character in an RPG. Aesthetically, you're limited to the options the designers provide. This may seem like a huge variety, but in the end you can only create characters that fit into the game's world. You can't create a toon character, can't create your own hairstyle, can't make a dragon, can't wear a T-shirt with your favorite logo on it...
When you create a starship or rocket, you often have the same kind of freedom. For example, in Star Trek Online, you can customize your ship with a variety of sections and colors, as well as the statistical customization coming from the installed hardware.
But in something like Kerbal or many of the new space combat games, you have a whole new level of freedom, where you literally assemble your ships out of base components. Sometimes the components are mostly aesthetic, but sometimes they have important functionality. Obviously, if the choices are functional, that both constrains and fuels your designs.
I prefer functional components, because they allow the universe to develop its own aesthetic. If your components are largely aesthetic, then players will tend to want to clone outside designs - weakening the uniqueness and flavor of your world.
Aside from that choice, the real difficulty is how you allow the players to create the ship in the first place.
The most common method in the next-gen space-fighting games is to use blocky components that can be stitched together. A less popular option is Kerbal's free-attach system, which has only been very lightly explored. A third option is the basically unknown option of being able to design the ship's contiguous spaceframe rather than building it out of component hull pieces.
The spaceframe is by far the most critical element of a good starship design, so let's discuss that.
Most of the most famous ships in fiction have a strong silhouette, a strong spaceframe profile. The popular "size comparison" charts show that.
We can actually learn a lot by looking at the size comparison charts. for example, most starships tend to be shaped like the part of a ship that is above the water, plus a shallower reflection for the bottom half. This is extremely common, even among the "box with flanges" contingent. Theirs simply look like barges.
Another common profile is one based on marine life. Fish and prawns are common inspirations. A few are based on the strut-and-module design of the ISS, which has a cool lumpy aesthetic. A few are also based on cities, which is kind of dull. A very few are vertically "stretched", using spherical or tower shapes that are as tall or taller than they are wide - very unusual, but most of them are simply tilted or stretched ship reflections. A few are based on basic geometrical shapes, especially spheres.
Of course, all of these are often heavily modified by protrusions such as wings, curls, or towers. In fact, the primary distinction between starships in today's media is the kinds of protrusions they have, big and small. We'll get to that, but I want to talk about the core space frame shape a little more.
All in all, by far the most common spaceframe is a navy ship with a muted reflection. However, this default is not necessarily the best option if you want to be distinct.
Most universes have some kind of preferred aspect for their ship designs. For example, Star Trek has nacelles. Warhammer has slooped noses. Star Wars has the wedge with the equatorial stripe. Eve online has the smooth-shell-over-complex-innards for a lot of its ships, similar to Rototech's biological wobbles. Freespace has the "n" curve to all their ships. Even within nonvisual media, you have unique elements that guide the ship design, such as the Honorverse's warships designed around the heavy energy walls their drives produce.
These aren't universal, certainly. In an attempt to make individual ship designs look unique, or to distinguish factions from each other, ships often do not conform to these standards. That's fine when you need to tell a story, but all told these ships have a particular design for a reason. Sometimes the reason is because the writer has a particular design sense. However, in many cases there are in-universe reasons for the ships to be shaped like that. Even if they are retroactive.
For example, the wedge shape of the Star Destroyer may seem arbitrary, but the reasoning for that is simply that the weapons in Star Wars do not scale. The Star Destroyer doesn't have any large guns to build its spaceframe around, nor does it have any single incoming cannon that it needs to armor against. Instead, it is studded with weapons and armored in general, because battles of attrition are the way capital ships fight in Star Wars.
On the other hand, the nacelle-oriented design of Star Trek's Federation ships is because of their warp engine technology. The design of the Zentradi ships comes from their pseudo-organic nature. And so on.
These are all functional reasons. The aesthetics are, at least in part, governed by an idealized understanding of how the ships are used. Sure, it's all made up and none of it tends to stick very well, but these are narrative universes guided by the writers. In a game where you create the starships, the rules of how the starships work will obviously be much more strict.
And therefore, the rules should give rise to in-universe designs.
The default "ship and reflection" spaceframe is just a fallback. When you don't have any unique ideas about how your starships work, you simply fall back on the tried-and-true "space is an ocean" trope. Instead, I recommend coming up with a unique mechanic or two that guides your ship creation.
For example, let's say that your magic technology is the ability to create plasma wings from a core module. You can't have anything in the way of the plasma wings: they don't magically appear around the ship, they actually emerge from the node, and happily cut through whatever ship components you've stupidly surrounded them with.
The result of this magic technology is that ships will be designed with a unique profile, depending on the kinds of plasma wings they are designed to deploy. You'll get teardrop-shaped ships sometimes, or figure-8 ships, or ships with a glowing spire... there are a variety of designs that emerge as you approach this technology from different angles and with different intents. But all of the designs feel new and fresh, because the technology is guiding the designs rather than the designs just being an arbitrary aesthetic choice.
This does not change the basic question: how can you give the players the tools to build these spaceframes?
Obviously, the biggest and most basic option is snap-together components. However, you will end up with a specific boxy look if you do that. Even if your parts are curves and slants and wings, you'll still have a chunky, broken-up look. There are a few other options.
One is to make many of the snap-together components have curves or slants that smooth out the boxiness. This is difficult to do using unchanging stock, but you could easily do it if your components could all be algorithmically reshaped to smooth and blend the profile of the ship. Still, that might be extra coding and art constraints you don't want to tackle.
Another is to allow the players to simply draw the profile, then fill it in using smart mesh creation. This is a lot simpler than you might think. You can allow the player to create secondary hull sections in the same way.
Another is to give the player a few default core hulls in common shapes, then allow them to heavily distort them using drag brushes.
All of these approaches can be combined in different ways if you really feel up to it.
The core spaceframe ship is not the only element that makes a starship unique. The surface of the starship is equally important and should not be underestimated.
Some surface elements are huge enough that they might even qualify are spaceframe elements. For example, the Star Destroyer's conn tower, or the many spires on the various spiny ships that have become popular recently.
Both of those examples are still surface elements rather than spaceframe elements because nothing is mounted on them. They are mounted on something, but nothing is mounted on them.
Surface elements are absolutely critical to defining how your ships look not in profile, but when viewed "for real". And they come in a wide variety, so let's cover some of them.
Color is important. Most universes prefer specific palettes, and within a universe every faction will generally have their own preference. For example, Star Trek is universally white with blue highlights for the Federation, and red with yellow for Klingons. Star Wars' much more navy-inspired designs were originally focused on functional gray, but later introduced a lot of blue undertones to the hulls.
Color is not just a flat wash, though. Not only do secondary colors matter, but the way in which they are put in matters. Star Wars capital ships commonly have a dark streak around their equator, for example. Star Trek ships have glowing panels - windows and phasers and nacelle equators. Eve's ships tend to use rounded rectangles of either glowing or dark patches to give a kind of an "office building of the future" feel. In Mass Effect, the colors are actual paint jobs, giving the citadel a very aquatic feel due to to the paintwork.
Surface texture is important, too. While nearly all ship designs have "smooth" surfaces at first glance, in truth the surfaces are much more complex than you think. First off, the smooth surface is typically riddled with detail elements such as windows, depressions, and sweeping plane changes. Secondly, there's often a secondary surface across much of the ship which has a different texture than the smooth surface. And thirdly, the smooth surface itself can have very different feels as to how shiny it is, whether there's subsurface scattering, and so on.
There's also planar elements. These are the surface elements which define the planes/surfaces of the ship. For example, the iconic Star Destroyer vs the Executor-Class Star Destroyer. They have much the same profile, aside from the Executor having a tapered engine section instead of a flat back. But they are very distinct from each other because their planes are defined differently.
The surfaces in question vary pretty simply between three options: flat surfaces, complex surfaces, and engraved surfaces. These three options are actually pretty much the same three options in any universe, but they are especially clear in Star Wars.
You can see the same three options in Star Trek's iconic designs, and see how they differentiate themselves from others. See, the Star Trek "flat" isn't flat: it's windowed. Star Trek doesn't do "armor", so their flat surfaces are not armor plate, but iPod-like smooth windowed regions. Their engraved surfaces are engraved with glowing phasers and energy traceries, while their complex surfaces are subdued intakes and connectors.
If we applied Federation surfaces to Star Wars' iconic Star Destroyer profile, we would end up with something that tasted more like Star Trek than Star Wars - the difference is severe.
Similarly, we can look at something like Eve's ships. Eve's flat surfaces are engraved armor plate. Their engraved surfaces are typically very wiggly topological contusions rather than the glowing lines of Star Trek. And their complex surfaces tend to be where the glowing parts come into play. In many games these days, the complex surfaces would be gun protrusions or arbitrary spines.
Now, we're defining these as "surfaces", not as "modules". While most games think in terms of mounting a cannon or a sensor dish, in terms of the visual design the two are equivalent and we don't care about the specific size the gun or sensor dish should be according to in-world rulebooks... we just put on a gun or sensor dish that fits the size of the surface we've defined.
Obviously, the ship needs to be built around core elements. Every ship has engines, for example. However, those are the original technological constraints we talked about earlier. The actual design process could be thought of as "how does this design want the core constraints? How does this design want the spaceframe shaped? And, finally, what surfaces where?"
Now we can think about how the player could design ships in that manner.
When the player has created the basic spaceframe, they can choose from a list of surfaces depending on their faction. For example, a smooth "crew deck", a "weapon mount" complex surface, a "shield rig" engraved surface, or a complex "science" surface.
The ship's hull shows a grid patterned all over - maybe a hex grid, maybe just a vert grid, or maybe a full-detail UV map. The player paints the surface onto the surface of the ship in whatever configuration they like. The resulting components are added to the ship.
If they paint crew quarters, the crew steadily increases. If they paint science, their science stats go up and various scanners are added to the exterior of the ship on that surface. If they add weapons, guns are mounted on the surfaces you paint according to the way you've painted. And so on.
This could even be made into a topological game. For example, painting a single square of surface gets you a light blaster. Painting three in a row gets you a forward-facing phaser cannon. Painting a "+" gets you a torpedo bank, and so on.
Anyway, there's some new ideas for how to let players build ships. I'm not saying these are the best ideas, but I would like to break the hold that "modules" have on ship design. Even small ships would use customized elements for everything - spaceframe, engines, computers, crew cabin layout - it'd all be custom. Just about the only thing that might be standardized are weapons, and then only if they need to use standardized ammunition.
Modules don't allow for the seamless customization ships should have.