See, that's just it: many of the ships ARE models in the prequels. Many shots of the Naboo fighters, Trade Federation ships, and others are modelwork or combinations of models and CG. If you watch in HD you'll see dents, scratches, burn marks on the ships.
You talk about "realness": how does a real Naboo cruiser fly?
To me, I can see many flaws in the old motion control work: bumps in the track, misregistered elements, matte lines, garbage mattes, awkward camera angles (due to having to mount the model), lack of track, poor lighting, etc.