Personally, I don't think that we should be designing technology to fit the vessel yet. One of the few advantages of Space travel is the fact that ships don't have to follow a design-plan as such, it doesn't need to be aerodynamic or even aesthetically pleasing, they can grow organically around the equipment they are required to carry.
At the moment, I think that's the best way to progress. Whilst it would be fun to have a replica Enterprise in Space, probably far more could be achieved in the way of advancing our knowledge of Space Travel with more 'equipment-centric' designs.