I agree with most fans of ff7 that the compilation did injustice to the characters by making them more cliche than the unique and intriguing characters they were in the original. However, the compilation did open up new areas in the story that could be used to make a truly awesome final game that will never happen. My point is, this post is pretty much just my thoughts on what they could do and if my post is starting to annoy you then you should probably turn away at this point before I got further.
The only way the story could redeemed is to forget all the other titles and instead of making any more sequels or prequels or even a remake of the original, they would have to remake the compilation into a game itself. How? Make cloud the main character, start of the original game. Keep the original game exactly the same in terms of the story and events, except make flashbacks a little more in depth to the point that by the time you return the Shinra Mansion for the final flashback, you've pretty much played through the entirety of Crisis Core. Sephiroth has to be the villain at the end of the game because no matter how many people hate him for no reason and throw invalid momma's boy comments at him, he is still awesomely evil. Again, forgetting all the Compilation crap, Sephiroth only died once, if even then, at the Northern Cave. The entire game you chasing/fighting clones of Sephiroth that Sephiroth was controlling while using Jenova's power to manipulate the parts of her body (In other words, the cells that were injected into the other experiments or clones). Remember that crystal the Sephiroth was suspended in when he forced Cloud to give him the black materia? That was the one and only REAL Sephiroth you did not face until the end of the game when you could finally return to the Northern Cave.
Why was he there? He was seriously injured by Cloud during the Nibelheim incident where Cloud actually stabbed him with the buster sword and threw him into the lifestream. Sephiroth, being the ultimate and most powerful being on the planet at that time was able to use the lifestream to begin to regenerate himself and through the lifestream ended up in the crystal of mako at the end of the game. Why should he survive the final battle with Cloud? I don't know, change the end of the original in this remake to make the real Sephiroth actually escape back into the lifestream as mentioned in Advent Children. Then make the events of Advent Children a short story mission where you fight a new summon as in a redesigned bahamut and maybe gain the materia after you kill the sephiroth clone (Kadaj), then go through the events of Dirge of Cerberus through Cloud's point of view, ending with Genesis coming back with weiss's body to do some wierd poem-related act with the final climax of the game involving Sephiroth, Genesis, Jenova and/or the Goddess (Could be the same thing for all I know), and maybe Weiss. One epic battle to end the entire series.
Pros:
Haters of the game will finally be glad its over.
The story will be wrapped up.
The additions of story from the other compilation actually wouldn't expand the length of the original very much.
Cloud will be more of the Arrogant, Awesome, and Hilarious character from the original and scrap all this weird half emo stuff. (For those who don't know, you actually got to sleep with Tifa under the highwind, although not shown but heavily implied, if you do the dating sim right.)
Fans will not only get a remake but the conclusion to the story.
Probably be the best game of all time.
Cons:
It won't happen.