*ZELDA SERIES SPOILERS*
Mana's opinions more or less align with mine.
The Ganon bait and switch was utter crap. Zant wasn't given much development to begin with, but he was a totally original villain and we had every reason in the world to believe that our troubles began and ended with him. In a final twist, Nintendo shoves him to the side so we can have a fight with our old nemesis Ganondorf, but ON THE WII THIS TIME GUYS. Mana's right on the money here. Side note: Most of the games that don't involve Ganon in any way are on handhelds, particularly post-OoT. It shouldn't be a surprise that all of Nintendo's risks are put into releases that really don't matter.
And on a personal note for me, the entire story seemed half assed in its presentation. Scenes play out as if the game is crying out to the players "LET US USE VOICE ACTORS ALREADY." Every character minus the big three and Midna were given minimal development and screen time even when they were supposed to be important. Link's friends from the village are mostly static, as far as I can remember. You're introduced to a team of "freedom fighters" who are out to help you on your quest, and the most they get out of that position is a few lines of dialog pre-dungeon crawl and all of them to collectively shoot a bird at the end of the game only to never be seen again. They wanted to introduce new characters and give them some depth, but in the end the depth is an illusion because the game doesn't want to detract from Link and Midna time. They couldn't decide whether the story should be up to snuff with the current generation or just enough to get by like OoT, so they did both and the result was an ugly mess.
*END SPOILERS*
To TP's credit, it had the best dungeon design and boss fights in the series.
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I like how each new topic you make reveals such varied facets of your idiocy. - foolmo
Now this is entertainment!