Kaguya has no real personality yet. We have no clue what she's like. Mostly she just stares blankly and seems almost... dumb? Like she really isn't thinking much, or is confused/mentally challenged.
She has a flimsy backstory. Sure, she's the "mother of chakra" and became conceited with her power, leading her to attempt to control everyone. However, we don't know anything about her motives in that respect. Until we understand more about her motives, and who she was before she became a "Goddess," we really can't appreciate her character (i.e, the character hasn't yet been written).
Madara was an extremely developed villain, with multiple arcs of backstory. He was developed for nearly 300 chapters, and hyped since the end of Part 1. He felt "right" as a final villain. Sad thing is, Kaguya entering the scene was coupled with the fact that Madara was Black Zetsu's puppet... and no one likes Black Zetsu. In fact, Black Zetsu has become even more annoying since Kaguya returned. There's nothing cool about black chakra-slime that worships its "mother."
The Obito/Madara duo was great. And they both did a good job transitioning into "Main Villains." Now we have a new duo, Kaguya/Black Zetsu, and neither of them has any significant development. Black Zetsu's "backstory" is just essentially hijacking every other Uchiha villain's backstory. All Kishi did was say "Actually, Black Zetsu did that. See?"
I want to get Kaguya flashbacks, followed by her killing off Black Zetsu. If she received some real development, she could fill Madara's shoes... til then, it's annoying. And Madara himself needs to come back at some point so he can get a proper send-off.