Madara had been built up as THE man behind everything. An Aizen if you will. To replace him so quickly and haphazardly with someone name-dropped a couple of chapters ago within the final battle is horrible in itself. It would still be horrible even if Kaguya was an ultra-charismatic well-written villain of great quality, which she most definately isn't.
I'm not the biggest fan of Madara, but we as an audience had some connection to him through the years upon years upon years of this manga building up to him. Kaguya is right out of the left field and nobody gives a slightest fuck about what she is and what she wants.
An overpowered Leprechaun from another dimension could have appeared as the surprise final baddie and it would have the same impact.