Mostly the huge way the Fused Shadows are built up in the first part of the game. And then there's that very dramatic, totally ominous scene in the Lanayru Shrine. That scene was built to foreshadow a dark plot twist, but for some reason that twist never came. As it stands, there is no point to that scene - it is extraneous fluff. It gives me the sense that the story was intended to go in a different direction that Nintendo ultimately decided against a little too late in the process. Your suspicions about the final boss make wonderful sense, and Ganondorf's inclusion would have been much more worthwhile if the battle against him caused the Fused Shadows to overpower Midna.

On the Midna for Final Boss Campaign - I made a thread on that when I first started posting around here. I believe my main statements went something like, "Ganondorf was lame," and "Miyazaki Midna as the final boss would have been EPIC!" . . . It didn't last long.

So what kind of signs did you pick up? I came to the conclusion because when I was playing through, I really was expecting it. The story seemed to flow in that direction . . . all the way until the final boss came out on his horse. Uhhgg.

http://www.zeldauniverse.net/forums/3052059-post13.html
Great post here, I very much agree with it. If it hasn't been done already, it would make a good thread topic. There are a lot of signs that seem to indicate Midna was originally meant to be the final boss, until late in the process Nintendo decided that was too much of a risk for the character.