So im not sure whether this idea is too complex to ever work, but here goes:
I'll explain using an engine as the example: you would have a 'base' engine part which essentially does nothing. Then you have lots of sub parts broken into 4 categories (i.e. Combustion chamber, Nozzle, fuel pump, gimbal). To construct the engine you take one sub part from each of the categories and add it to the base part.
Then depending on which sub parts are chosen, the engine has different characteristics (Fuel / ISP / Thrust / Mass / Gimbal range etc etc) and visual appearance. Some of the subparts wouldn't be compatible either, so you have to make sacrifices - like if you want ridiculous gimbal range, you have to sacrifice on mass or thrust for example.
Im not sure what other parts aside from engines this could apply to, maybe command pods and RCS would be ideas.
I hope i've explained that well enough - now i've written it i seriously doubt its possible to add, but I'm curious.