I'm afraid I have to say no.
When I first read about Twilight Princess, it seemed to me that Ganondorf was thrown in haphazardly. Then I actually played it, and it seemed alright until the end. Something was wrong. I couldn't figure out exactly what it was at the time, but something was just off with Ganondorf and the game's climax.
But I've been thinking about it, and I have a few points...
The game set up Zant as the villain. His story had a lot of buildup, including his assault on the world of light, him usurping power and transforming the Twili into Shadow Beasts, his relationship with Midna, etc. It was quite cool, and incredibly dramatic, and then it was all flushed down the toilet. Boom, Zant was a puppet and Ganondorf is the real evil. It was... weird and rushed. Not done very well at all. They could have pulled it off if they set up the story a little differently, but they didn't. It was especially weird, because it really felt to me that they intended Zant to be the villain, and then reworked the plot a little to fit Ganondorf in. Likely in an attempt to be more like Ocarina of Time. If they spent more time on it, it could have really worked, but it seems like they rushed it. (You know, in general, it seems like the game just needed more time.)
Then Ganondorf appeared. Despite him being mentioned a few times prior in the game, his inclusion was still more along the lines of a "final boss switch" in which the game randomly throws a new villain at you at the end of the game. It's typically a weak plot device.
But there was another thing. Ganondorf's inclusion wasn't just a downplay on Zant. All the game's drama and buildup was centered on Zant and Midna. Not Ganondorf. What this means is that when he did finally show up as the big bad-***, well, it was like "who?" Obviously it wasn't quite like that, as we all know who he is, but you get my point. Suddenly this new villain is thrown in. He's stated to be this big bad villain, worse than the guy you thought was the real villain, but in essence, he's just a shallow plot trick. Because there's no buildup. No stage setting. Nothing. Just "Oh, Zant wasn't the real villain. Go fight Ganon."
It sucks, because it makes both Zant and Ganondorf less that what they could have been, and in a way it's a disrespect to both characters.
They should have spent more time on it, or kept Zant as the main villain. Because, I'm serious. The Palace of Twilight was the games climax. In both plot and feel... to me at least. Hyrule Castle was more like... a bonus stage.