Don't forget that the creator of Mario and Zelda, Shigeru Miyamoto, also created POKEMON! So now you either hate him or love him.
By the way, the only reason that Zelda is being made fun of is because one, the YKYPTMMGW focuses on Mario related stuff. Two, it was someone else that brought up the topic of the whole Shiek problem.
The truth is, Zelda isn't trans-whatever. The truth is that Zelda is a tomboy, as was said by the Truth stone in Ocarina of Time, so she dressed up as a boy to fool Link and to help him on his quest.
Zelda did not have any crazy stuff done to herself for that Sheikah transformation. First, she probably used contact lenses, since Sheik's eyes are different from Zelda's eyes. Second, Zelda must have done something so it wouldn't be obvious (I'll leave it to billy chilly, since he isn't afraid to talk about these things).
And like I said before, it would be scary if Bowser was a "tomgirl." So let's not think of that.
To be a Koopa, you must become a Koopa.