Few issues here -- why exactly does Fi decide to just leave? She was a pretty convenient character, though Skyward Sword didn't give her much depth other than being a computerized Navi. It doesn't make practical sense to me exactly why she had to disappear into the sword forever. Future Links would've surely appreciated her help. The game says that she must return to the sword because her mission is complete, but that seems like a bogus reason to me. Lazy scriptwriting? For that matter, the whole ending from returning to the past up to the credits seemed sort of rushed to me. I did enjoy the final few fights, but I felt like Demise should have been an epic drawn-out marathon fight like the final battle in Twilight Princess, though perhaps I just had too high of an expectation. The first Ghirahim fight and the Demise fight were one of the few times I've felt real adrenaline in a one-on-one battle in a video game since I was a kid, just because the characters were so annoying to battle, and they felt so sinister. Tl;dnr: epic ending, but it still felt lacking.
Now that the rant is over, a few questions. Demise says his incarnations will return again and again. So the most obvious implication is that Ganon is a form of Demise. But does this also imply that other Zelda villains such as Vaati are also forms of Demise? And the other point that bugged me was about the map; the different areas of Hyrule are separated by provinces, but the names don't return until Twilight Princess. I'd like an explanation of what happened to the provinces during Ocarina of Time, and why the names came back in Twilight Princess.