Well, to be fair, Madara was completely blind-sided and caught off-gaurd. Plus, she was dead. The black Zetsu is just her condensed will. She'll probably come back though, after taking Madara's body that had the Jyuubi in it.
That, along with the fact that Madara was the only one able to awaken Rinnegan makes him the best candidate, since Kaguya was apparently dead.
Originally posted by Tzeentch
http://www.killermovies.com/forums/showthread.php?threadid=24981&pagenumber=1489#post14738578
Well, Madara being the big bad was the most boring thing in the universe, so chumping him in favor of any character (even one that was an afterthought) is ok in my book. I did remember saying something like "I'd rather have Black Zetsu killing Madara than him being the big bad". So, eh, called it.
Can't say I care either way 👆