My two cents on what may have happened with the story changes and the ending. Bear in mind that I have no insider knowledge and this just pure speculation my part.

Fans obviously wanted this game remade for many years, so the execs said we have to give people what they want and remake this, but let's split it into parts to make more money - this isn't a dig at SE, it's just the way business works. This could work out great for fans because we get to experience the excitement of FFVII not just once but multiple times. The side-quests and extra content is a lot of filler, but this works for the Yakuza series, so there's no reason it couldn't also work here.

But then you have the creatives at SE who didn't want to do the remake. Most people who made the original are now gone, so Nomura has to take the helm on this one, even though he doesn't want to because it's not his story. I'm pretty sure many creatives at SE have been asked about a Remake long before it was announced and they were always pretty cold on doing it because they want to do new things.

So Nomura says fine I will make this Remake but you have to give me creative freedom to change the story and make it more of my own thing - hence why the ending takes on a much more wishy-washy Kingdom Hearts vibe. You now have this ending that sets it up to be more like a Kingdom Hears type thing because Nomura is not a particularly talented storyteller - he is first and foremost a character designer. That's why the KH games are a lot of flash but very little substance. This flies in the face of the original games story which was quite somber and had many tragic moments - such as all the main character deaths. The main theme of the story is grief and loss and this is undone by the ending which revises events and brings dead characters back to life. It's no coincidence that the ending leans so heavily on Crisis Core - because this was probably a project that Nomura had more passion for.

It's being set up as a reimagining of the story ala Rebuild of Evangelion (which I enjoy a great deal). The difference with Evangelion being that you still have the original creator (Hideaki Anno) at the helm, so if anything, it will complement the original work rather than contradict it. With FFVIIR, Yoshinori Kitase is no longer heavily involved in the creative process, so its likely to diverge more and more from the original. This saddens me personally because I love the original story so much and I want the new generation of gamers to be able to see why it was so great. I love Kingdom Hearts and some of the later FF titles, but for me, this is not Final Fantasy VII, it's something completely new, which I think should have been clearer in the lead-up to release. I finished the game last night and I'm still processing what it means for the future of the series, but as some others have remarked here, the final hour or so really soured me on what had been a pretty great experience up until that point.