Well, I'm not getting my hopes up about them appearing in more than just this part, but I would love it if they alter the story of at least one character and have then appear in future parts as well.
I am assuming from the start that the story will be heavily altered. A lot of people are treating this as a 1/3 of a game or "5hr of actual story with a lot of filler" and that is a very sad way to look at any remake. The story we know of FF7 is irrelevant, this is gonna grab that and just throw in some big modifications to stablished areas and characters as well as introducing new areas and characters. Its gonna be a new game based on an old one. A proper remake.
We dont know how the original story will be divided - (but assuming is fun) - im assuming that the first part will end in the main characters leaving Midgard and Shinra will be written as the big antagonist of the first game, with only references that Sephiroth is around until the very end, cause in my head that'd make a lot of sense and its a natural story wrapping up nicely, so in that sense I can imagine they'd alter the story in ways that fit that logic. Like leaving Red completely out of the first game for example, or simply having supporting characters come back to the later episodes for simple continuity... Like, lets say, Biggs and Wedge (and Jessie by proxy)
Since every FF has to have a Biggs and Wedge.