Some ship design jewelry ideas:
-Items with race logo on them (panels, fins, etc.)
-Special effects. I know the elec arcing is part of the game to show a ship is damaged, but having the ability to add elec arcs, glowing engines, pulsating lights, oscilating panels, etc. would be killer sweet. Obviously, more system intensive. Think the disruptor array and nacels on the Enterprise, or the Kitt light on the Cylon ships in BSG.
-Mobile parts (again system intensive)! Having that big ring actually ROTATING would be flipping sweet!
-Parts that connect two hardpoints, and sizes to fit. You can kind of cheat this effect now, but I think it would cool to just have a series of bars, tubes, etc. that automatically connect one end to a hardpoint and you click on the second hardpoint for the other to connect to, and it does, stretchin/resizing as need be.
-Glowing parts. Not so much as the special effects item above, but more so parts that have similar qualities to the engines having a color, but obviously NOT an engine part. For instance, rods that connect main bridge to the mid section... all glow the same color as the engines.
-Rotateable hard points that hold the same direction. More accurately, the abillity to alter the horizon of a hard point, while maintaining it's direction. Make it intervals of 15-45 degrees.
-Delete key functionality!
-ability to turn off hardpoints (mentioned in another post) for viewing.
-the ability to delete pieces that DO have other pieces attached. this would make it less tedious to take back 5 or 6 steps of poor choices. A confirmation box would eliminate accidental deletions.
-a more discernable Bridge
-more items that are round or sleeker (aside from the more curvacious Torian pieces)
-add the ability to "skin" over pieces. Many of the pieces, regardless of scale, don't "fit" right due to slightly different textures. So maybe allowing a secondary "skin" layer could be added to add some smoothness to design and blending of textures.
-potential to add "damage" scarring textures on panels. I'm just thinking about all the cool star wars vehicles that ust wouldn't look AS cool without that blaster mark there, or scrape here.
-kinda of similar to my race decals suggestion, but how about numbers and letters as decals.
-more impressive engines! The only one that LOOKS like it could make your ship run like a bat outta hell highest level Ion drive. Hell even the high-end warp drive looks un-assuming.
-different texture values. kind of falls under the skinning suggestion, but the ability to choose different base textures could be fun. For instance, the chrome look like Amidala's ships in SW: Ep1 & 2.
-this is a stretch, but perhaps allowing to make parts transparent could yield some interesting results. have the stipulation that the HULL cannot be invisible... thus eliminating having ghost ships.
Those are some seeds that spilled outta my noggin... hope some of them spark some inspiration!