7 designers work for the LSW team. Each has an area of expertise, I'm pretty sure one does shuttles exclusively. they decide what they want to make, and a prototype. Lucasarts has to be satisfied with the model, when the separatist shuttle was in the making it was originally going to be made to look like the one that appeared in RotS, but lucas then wanted to appeal to their TCW fan-base and altered the reference. The designers are more independent than one might think, they decide on minifigs and sets, but Lucas must approve the set before it is released. They always have the final word.
Think about all the qualities that would to be implemented to please all their audiences, if you cna design a MOC that meets all those standards, then I'll listen to these complaints and see them as valid. It's harder than you might think...