One thing that has been kind of getting in the way of my ship-crafting is that there seems to have been a few assumptions being made about the manner in which some parts will be used, as if their functions have already been assigned to them even before the players touch them.
For example, there are a few vaguely saucer-shaped parts where the assumption seems to be that they will only be used in the same manner as the saucer section of a Star Trek ship and, as such, there are no attachment nodes on the outside of the saucer; at best, there might be one in the very center.
And that makes building something like a UFO suddenly a lot more work, since it will require offsets at the very least, if not rotations as well (which are, in and of themselves, quite a lot of work because you have to manipulate numbers instead of having something to grab with the mouse and drag as you'll find in most 3D modeling software. Knowing which axis rotates in which direction often requires a fair amount of trial and error since there are no indicators.)
The objects that resemble weapons have no attachment nodes at all, which makes building a ship that is basically one giant cannon rather difficult since achieving symmetry requires a fair amount of offsets as well.
One thing that might help this is if we had a null-object: something which did not render in-game, but to which objects can be attached. Since we're only allowed one base object to which all other objects must be parented, starting with one of these could be a big help with the symmetry problem.
...I suppose it's possible that this is just the 3D modeler in me--the part that's used to using 3DS MAX--coming out to play, but I honestly do think that the ship-crafting could be made a bit more user-friendly in this regard.