1st of all you make a huge misconception, which destroys your entire discussion... Anyway I will come to that.
Regarding Nagato, it is mainly due to creating a plot, but also Nagato probably didn't know about rinne tensei. I mean the jutsu comes with the eyes, but the know-how may not come with the eye. We don't know. Madara could have studied it long ago, so it is obvious he knows it. Obito could have told him how, or black zetsu could, who knows, it doesn't really matter.
Rinne tensei is somehow time-dependent, you could say that it brings back the soul of the person who died, BEFORE the soul passes on to "the next world" or whatever it is. I know why you don't think so, but Nagato said it himself, he can't bring back people who have been dead for too long. Obito obviously knows this too..
Then how can he revive Madara? We don't know that yet, but lets see if Kishi will explain it. If I am right in my assumption about the soul passing on to another dimension, like we see in Kakashis flashback, his father said "looks like it's not your turn yet anyway" or whatever, the point is, Kakashi was in some "medium" which wasn't really existing anywhere, lets see the world as 2 universes. 1 for the living and one for the dead, then Kakashi was somewhere in the middle with his father for a short time. He would have moved on, but rinne tensei prevented this before he could move on. Also it seems there are exceptions, like with Kakashis father, who didn't move on due to his feelings he wasn't able to.
This is actually prove enough. Cause that would technically give Madara a possibility for revival through rinne tensei. What if Madara found a way to prevent his soul from moving on from this medium, which is the world between the worlds, or whatever I described it as above. That would allow this. Such a place does exist. We already know. AND I happen to believe that this "world" is somewhat connected to many things we have seen through edo tensei. If the person who was revived came from this "world", which kakashis father was stuck in, that could possibly be because of their feelings for something they have done, or something they needed to say, or whatever. This was also somewhat described by Dan, as he got to say goodbye to Tsunade for a last time. Anyway my point is that all the persons that was able to release their edo tensei on their own, they weren't really "dead", they were simply on their way to wherever souls go after they "physically" die. So what I am trying to say is that if a soul is in a special emotional state it is not very stable, it will have an urge to move on, which is why it was possible for a number of people to break their edo tensei on their own, as they were relieved of their "pain" or whatever was nagging them.
You may ask yourself about Rin, but first of all, Obito didn't get rinnengan until very late, and it's not like he had any chance against nagato. Also how could he possibly not do as Madara said. He was in a huge need of the zetsu suit in the start, and if he didn't act according to plan, zetsu would probably stop helping him. Where would that leave him? Besides Madara talk no jutsu is strong U_U
