I couldn't agree more. Since I see Ganondorf as the most epic villain ever I think TP should have based most of the game on him if they were to put him in there, but I think the reason they put him in was to create a surprising twist in the plot and make a point where things either become much...
I actually love it when they use Ganon. I feel that the game will make more of an impact of the Zelda storyline with Ganon in it, since he has the triforce of power. But maybe thats just me