The original story is so much better. For a start, it actually explains why you visit old areas. The phantom ruby is so confusing and nonsensical in Mania. Another change is I'm assuming the original story would make it clear that Eggman and the HBH are enemies at the beginning. While in Mania it isn't at all apparent until right at the end. I'm wondering when the story was changed. The old story seems to line up with what Whitehead was saying in the earliest interviews after the games announcement.