When you instantiate an object is there a way to transform it's scale?
var instantiatedPrefab = Instantiate(somePrefab,transform.position,transform.rotation) as GameObject;
instantiatedPrefab.transform.localScale = Vector3(1,2,3);
Just set the localScale on the resulting gameobject's transform
you can create a play on wake animation on the object, that transforms it to the correct size