Times have changed. I know this saga doesnt continue your exp levels and builds between releases but nowadays I don't want a playable character to be removed from a game permanently. It was accepted in the 90's, building your char, using for hours and then suddenly you had to deal with a party breaking up. Many games did this, forcing you to use chars you never planned to use.
The difference as I said is that it will happen at the very end, and part 3 will likely start from zero yet again. But still, it would mean Part 3 to omit a very popular character and I doubt modern day Square is going to roll with this. They're even looking for ways to incorporate Zack now.
I think one of the very reasons this trilogy takes liberties is so they have an excuse to change these events.