My feeling is that they will keep the integrity of the overal story. It's kinda impossibly for them to not do that. From what I seen in the recent trailers, my thoughts on surprised are gonna be more about, oh this reminds of such and such in the original. There is too many parts of this major overarching story for them to skip out on or alter to much. It would have to much impact on the rest of events ahead.
That said, I do believe we will see a lot more content in between parts. I am sure they over analyzed what exact parts are vital to the story. So anything in between is atleast fair game for them to expand the game. Another point of interest is likely story depth. While none of us want to see story changes, there is more then enough room to make stories more detailed. Such as avalanche really being portrayed as terrorists or shinras propaganda machine. The motivation for barret is clear, but what of biggs, wedge and jessie? Why are they doing this? What got them involved?
Personally I see avalanche as the best and easiest expandable material. My guess the bulk of the game will be leading up to the plate getting blown to bits which will set in motion the "endgame" for part one. That said, there most likely will be an endboss or atleast something that will end our time in midgar. I have a feeling that will be slightly different then what we expect. Mostly cause they will need to have everyone sit up in their seat wanting more. So they might tease the outdoor world, there is never gonna be a long ass chat in kalm, atleast I think they will use this chat as a gateway between part 1 and part 2. I could also see them not giving us a "motor cycle" exit, but rather have the motor cycle exit or well escape from midgar the introduction "bombing run" of part 2. Just to have a reminder of midgar and where we came from when part 2 is finally here. That would make the motorvihicle the first boss in part 2. I would be very happy with this.