Maybe Madara is just much more skilled with the Rinnegan/Gedo Mazou than Obito is. Only real explanation and its only natural Madara would be better at it.
Well he did mention that he was trying to find an answer in Naruto. Extracting Kurama would incapacitate Naruto and there goes his answer.
He could've gone after Bee but he simply didn't just like he didn't go after Madara the.moment he gained control. If he would've dealt with Madara back then, the war would've probably been over but it simply didn't happen.