I would mainly chalk it up to the second half of the game being a complete rehash of the first half of the game, as in collect two dark magic shards of something by going dungeon-to-dungeon, having a mini-adventure in-between that and the third piece of said item, and then one last temple and major twist. (Although there was an extra dungeon in the second half due to Hyrule Castle.) Going along with that, the dungeons in the second half of the game (save Snowpeak Ruins) were basically just boring and stale. (Snowpeak Ruins was somewhat boring, but it was a very unique dungeon in that it utilized the Compass to where it was basically needed, and the dungeon was almost all puzzle-oriented.) Each of the dungeons in the second half of the game were very unique in style, but they just weren't executed properly, whereas all the dungeons before them were executed perfectly.
The other main thing, though, would be that Ganondorf was in the game, which I hardly consider a fair reason. People were all like "Oh, great, they're just re-using Ganondorf again because he's the 'main villain' of the series. Man, come on, Nintendo, putting Ganondorf in just ruined Zant." Some people look at it as in Ganondorf coming in was just something that ruined the originality of the game, as it made Zant to where he was no longer the main villain (although I fail to see a complaint about that with Vaati in FSA). They felt it ruined his sense of mystery and fear-worthy attitude just by being implemented into the story (which is not true). While Ganondorf was brought in very nicely, -- and for reasons that made complete sense and were very legit, such as Zant obviously having to have
something behind his shocking power -- the whole second half of the game, neither he nor Zant was even remotely mentioned, which made the impact of Ganondorf being introduced fade, and, sadly, did make Zant feel a little less powerful. If Ganondorf had been revealed later in the game, I think people's beef with Ganondorf wouldn't be near as bad, if there was any. Another reason would be that Zant was made into a pathetic, completely insane lunatic that could barely hurt Link, which was totally contradictory of the effortless Zant we had seen before. I feel that this made facing Ganondorf just added onto all of the other things mentioned, and that it also was just a major factor itself. It made the buildup to finally taking down Zant a major letdown, and therefore made the climax to Ganondorf with a disappointed and somewhat angry tone, as Zant's character had been completely jacked up. (Xinnamin says it was due to him being obsessed with Ganondorf, but he would have already been obsessed with him before that imo, so I don't agree with that.) However, I think the biggest reason people didn't like Ganondorf in the game would be that...wait, this is kind of off topic. Well, sorry to cut off my awesome ramble (heheh) at the best point, but these points are already in another thread (
http://zeldadungeon.net/forum/showthread.php?20433-Do-You-Feel-Ganondorf-Was-Tacked-Onto-TP), so I don't need to finish the end of it, as I've already said them there.
Anyway, all this to say that I can understand why some people were disappointed with Twilight Princess (and why some, sadly, disliked it), but I feel that some of the accusations (if that's what they can be called) against the game are a bit harsh and unfair. Sure, Twilight Princess has its flaws, but so do most games, and I don't feel the flaws ruined the game. It just took out a bit of the game's potential of being the best Zelda game yet.
