I agree with your points but I'll take the game as it is for now since it's not completed yet (though I wish they wouldn't do this anymore for future games).

(SPOILER)
I've had a lot of gripes about the padding in the game - I felt like a lot of it could've been reduced to side quests and just release a full-game instead part of a game. I think Nomura wanted to do something different with the remake and added a timeline split to the mix. Essentially, what I got from the ending was that it won't exactly track the original FF7. There are subtle differences and some key differences that happened throughout. Aerith & Sephiroth seem to understand their fate through whispers and we see flashforwards/backs of events from the past game and the prequel. It seems Aerith knew a lot more than she was letting on and the Sephiroth we encounter knew what would happen as well. I'm in the camp that part 2 might be very different from what we expect from the original FF7. Maybe that's why the pacing and story changes were what they were.