I imagine something like the following:

Component description format
Model description format
Model generation rules description format

Simple human/machine readable/editable formats based on JSON, YAML or somesuch.

Component description format file accompanies an image file of component sprites: describing geometry, connection and classification data for each component.
Model description format specifies a model assembled from components, describing the component heirarchy.
Model generation rules description format specifies further restrictions beyond the full set of permutations.

GUIs like you describe to help create component descriptions and model description would certainly be cool too.
 EDIT: Grr! How do you post code without the whitespace getting stripped? Component description example
[
{
"id": "wing1",
"bounds": [[0, 0,], [64, 64]],
"classification": {
"type": "wing",
"handedness": "left"
"mirrorable": "true",
"faction": "pirate"
}
"connectors": [
{
"id": "base",
"position": [64, 32],
"normal": [1, 0]
"required": "true"
"classification": {
"type": "wingSmall",
"handedness": "left"
"gender": "male",
}
},
{
"id": "weapon1",
"position": [0, 32],
"normal": [0, -1]
"required": "full"
"classification": {
"type": "weaponSmall",
"gender": "female",
}
}
]
}
]

Model description example
{
"id": "Billy's cool pirate ship",
"mirror": "true"
"root": {
"id": "chassis3",
"connections": [
"cockpit": {
"id": "cockpit76",
"connections": [
"weaponLeft": {
"id": "laserSmall",
}
]
}
"engine": {
"id": "engine4",
}
"wingLeft": {
"id": "wing1",
"connections": [
"weapon0": {
"id": "missilesCluster",
},
"weapon1": {
"id": "laserMedium",
}
]
}
]
}
}