Apart from the factors which you mention, some of which pertain at least in part to the software and not to the hardware, it's also a matter of how the bodies are physically manufactured. For instance they can be weather sealed, they can be more or less robustly built, they can be made of "cheap plastic" or of magnesium alloy. In addition, any given model is tested for a certain number of shutter actuations (there are some very interesting questionsquestions and answersanswers on this).
As a final issue there is ergonomics and interface: factors like weigth, or how does it fit your hand or the buttons/commands are placed can affect very strongly the result.
