I'd like to have Goku involved in the fighting in some capacity, if possible - he wouldn't involved in the end of the plot, given that he lacks anything holy to do major damage to Ganondorf with, but I'd think that Goku would be able to slow him down or keep him from killing people, at least. If there's too much going on with Ganondorf as it is, he can fight mind-controlled people or animals - whatever works.