Nomura said the spirit as well as the characters will be faithful to the original but the story is "reimagined" because they think it's redundant to have an hd remaster of the original and a full blown remake telling the same exact story frame by frame, and I'm OK with that. It will be fresh, but familiar at the same time.
I heard some people think they might be more involved with the story since Square didn't have enough time last time in the original. I remember getting Yuffie was a pain in the ass...
Yup, while it was an interesting, yet annoying, way to get her it would just be better to write both of them in instead of finding them up to chance.
I also heard that the cross dressing part would be staying in the game as well as others similar to it.
http://www.vg247.com/2015/06/17/final-fantasy-7-director-says-please-look-forward-to-crossdressing-cloud-in-the-gritty-remake/
Crossdressing Cloud might be kind of scary in new graphics...he was OK in PS1 graphics. Yeah hopefully both Vincent and Yuffie are written in the story more and not hard or annoying to acquire.