They refer to him as Ganon when he is in his pig form. When he is in human form he is referred to as Ganondorf. Yes I know people tend to just call him Ganon for short but maybe Nintendo is trying to be slick with us. We don't know for sure.
Umm, what's wrong with having him in the game? And anyway it's just a possibility. We still don't know much about the game to even try to make such points for either side. It's always been Ganon/dorf vs Link just like it's always been Bowser vs Mario. So why not? How would it make the game...