She was never controlling madara, up until now he never knew she was part of the tree and up until now he never acquired the power necessary to meet her or circumstances necessary to meet her. This is no different from naruto and sasuke meeting and getting schooled by the sage and given a power up. Why can't madara get another power up? That's what your really a *****ing about.
That's the thing though, Madara never needed another power-up. Wtf happened to PS that is supposed to be distruction incarnate? Wtf happened to his Gunbai that can reflect all ninjutsu and create protective barriers? Pretty sure the Gunbai would have been able to reflect that rasenshuriken if it could reflect a tailed beats ball. And wtf happened to preta path? Explain why Madara doesn't just absorb the rasenshuriken? It has sage mode? Madara can control freakin sage chakra he stole Hashirama's didnt he? Why does he not just porn Gai with that super ridiculously huge PS of his? Why does he not reflect Naruto's jutsu or absorb it? Oh ya coz hez Gunbai mysteriously disappeared off panel and his rinnegan can't absorb ninjutsu anymore for whatever reason. I mean, it was fine when Obito couldn't shift through dimensions because of the Juubi, okay it wasn't, but it was tolerable, but there's no excuse for Madara to become weaker as a riinegan juubi jin than he was without even his eyes.
I understand that it makes sense that Madara meets Kaguya if Naruto and Sasuke meet the sage, it is a perfect plot. But the way in which it was done was ridiculous, I mean this is the guy who was dropping meteors and chopping mountains off, now he gets pawned by such lower level ('lower', not 'low') techniques? It's a joke