All-Killing Ash Bone is countered by Almighty Push, Preta Path, Limbo, and chakra arms.
Eighty Gods Vacuum Attack is countered by chakra arms, as Naruto has shown.
Expansive Truth-Seeking Sphere, if she can even use that without disruption, is irrelevant since she has to be within 70m of it to control it, so it's a suicide attack and they both will regenerate eventually.
Limbo outnumbers Kaguya in close combat.
Sasuke's Perfect Susano'o almost had the speed to slice Kaguya, so Madara's should be more efficient with his abilities as well.
Sage Art: Storm Style: Light Fang can only be barely dodged by a fully concentrated Naruto, so through distraction it can be effective.
When it comes down to it, Madara will win in strategy when both of them can counter each other's moves very well. Madara also has far more variety of techniques to choose from.