I'd go with whichever has the nicest kitchen/family room because I bet that is where you will spend the majority of you time over the years. It will be the hub room of the house.
If one of your bedrooms is spare, I'd fill it with shelving and have it as a store room for all the stuff that never really has a proper home.
Also, if it's not build yet and you are certain you'll plaster up the dining room wall, ask if they'll build it like that.