I seriously doubt that MS is going to recoup the money they spent to get SE to port over FF13. Remember, MS paid for this port while Sony did not have to.
To take that money they HAD TO make the two games similar, it only makes sense. Is it fair to the PS3 crowd? Sure, no telling IF (and i repeat IF) this game never went multiplat that they would have kept any of this anyway.
The only limitations they MIGHT have had by making the game exactly the same is having to deal with arcade units (making it so the game does not have to install) Other than that, unless we hear anything directly from SE about this, we will never know. People keep talking about dual audio tracks and whatnot. Have they ever done this? (I have played every single one and I dont remember any of them having this option, tho I could easily be wrong). It is highly unlikely they would have done it anyway.