You go the timeline messed up.
The akatsuki was made before yahiko died.
Yahiko founded the akatsuki and tobi said that he urged Yahiko to make it.
how would nagato know that kushina was the kyubi jinchuriki?
Well maybe he wanted to take revenge for Rin's death or something. He also probably did not think that anyone would be able to stop it. (He is pretty stupid for that) He also had control of it so maybe he thought that if things got bad he would just tell the kyubi to run away or something.
I know how everyone is saying kakashi is crying so he killed rin. here is my theory on how this could have happened.
rin dies in the onslaught but kakashi somehow manages to survive and when the zetsu transforms into rin, kakashi kills it and starts crying due to the fact rin died or...
I think Sasuke is going to stop Madara.
It is a possibility as in this picture-
http://www.narutobase.net/manga/Naruto/592/11
He seems shocked that Madara is still around and on the next-
http://www.narutobase.net/manga/Naruto/592/12
he seems to be determined to do something.
Just my opinion and...
http://www.narutobase.net/manga/Naruto/446/9
i dont know if any of you noticed it but it says-"after three years of training, we had grown stronger in body mind and body"
i know its really random