You definitely make good points, and I can see where you're going with this. However, I must say that while the pacing was definitely odd, I think it might have gotten to be too much if they'd fleshed out every single battle. I liked that they focused on the first one in order to create the mood, and then didn't flesh out another battle until the battle with Ganon. If they HAD fleshed out all of them, it may have detracted from the impact of the final duel.
Also, a few things you may have missed: The Shadow Demon was the "poe" they put in that bottle. This was likely both a reference to the game and an answer as to how an elemental demon could be defeated. Another thing, you keep saying that Shiek being Malon would have been a better ending, but are you suggesting they rewrite the script completely, or did you miss what Talon said during the dinner scene about Malon's death, and were confused about what happened to her?
Personally, I've always thought that in the games Zelda's personality was a bit flat. I liked that she actually had emotions in the movie.
Other than these points, however, I agree with most of what you said. However, I cannot say I am swayed in my opinion that this is my favorite movie ever, even if only for the fact that Ocarina of Time has had such a crucial impact on my life. Instead, I feel that this movie has in fact given me a new taste of the same game, in the same way that I felt the first time I took the 3-Heart/minimalist challenge.