0. Tobi/Obito isn't trying to destroy the world, or kill all people. He, in his own way, wants to put the world to peace. If he manages his Moon Eye Plan, there will be no wars, no deaths, no disappointments, no responsabilities. In an illusionary world everyone will be able to live their own dream and they'll be safe from all Pain. In other words, we can say Tobi is trying to save others from the Pain he had to endure once, and aditionally he wants to put his shattered heart to rest in this sweet, endless mirage. If you look at him, at Obito Uchiha...he seemed to be a failure from the very start: nothing he tried to achieve came true. He couldn't confess his feelings to Rin, he was beaten by everyone, he didn't become hokage...on the brink of death he finally thought he found someone that would carry on his greatest dream: protecting Rin and making her happy. He was convinced that this one, only time, he wouldn't be disappointed because Kakashi has always been something, he, Obito wanted to become. He had strenght, so nothing was impossible to him, in Obito's eyes. But that dream has been shattered too, in a milion pieces, when Kakashi let Rin die, while he survived. We don' know the details, but Kakshi may be at fault here. Maybe he didn't follow his heart, myabe he hesitated...who knows? Then just imagine he meets madara who tells him he can create a world where there is no need for dreams, because you can have anything you want right away: no regrets, no pain, only happiness and fulfillment. If I were Obito, a great failure from the beginning till the end, i would be tempted by such a proposal. I see Obito/tobi as an anti-hero: an anti Naruto: they were the same: emarginated, not gifted and they failed everytime but had the determination to stand up and go on. Obito tho' was hurt one time too much, unlike Naruto, who, too was on the verge of becoming an antagonist. In that instant when Iruka acknowledged him, he saved naruto from the darkness Obito fell in. Otherwise he would have just put on a mask, called himself Kyuubi and he would want to crush the village that made him suffer so much...then, filled with great void, he would want to put his emotions to death, in order to feel good at least. As in naruto/sasuke's case, even naruto/Obito's roles could have been inverted now.
1. My bet here is this:
Madara Uchiha has been observing Obito for quite a long time. I assume he had fun spying on his clan since he left, in order to see what would they do without him. Then he sees this little boy, Obito. The boy is a big fuss and is the clumsiest uchiha Madara has ever seen. However he has a strong will and many dreams. Madara, already hardened by his own experiences, observes as his ambitions fail step by step. From the beginning he sees him as someone who will be easy to manipulate. Obito wanted to be hokage huh? I bet that impressed Madara too: an uchiha who at least wanted to ascend at the top ranks, to power, like he once wanted to do. In a certain sense he recognizes his ambitions in this boy. Then Madara sees Obito's final wish expressed before being crushed by the boulder. If the wish weren't fulfilled, obito would surely fall into despair and he could then use the darkness in him to manipulate him. He then himself arranges Rin's death. kakashi is strong, but if Madara plans something, a small ninja like him cannot do anything. Suppose in the meantime, the recovered Obito has no right leg and right arm, so he can't move...and he's barely alive. He needs to recover in the meantime. Madara then, collaborating with orochimaru, creates Zetsu, and with this he can heal Obito. Then he tells havhim about the death of rin and stuff, so Obito awakens MS. Obito might have wanted to challenge kakashi, or even kill him in revenge, but Madara said that he has a better plan, and reveals him the futility of reality and how much better would be to live in the mugen tsukuyomi. Then he puts him under genjutsu (something like Tsukiyomi that can make you spend countless days in a blink of your eye. In that period he trained him hard, within the illusion, he showed him everything about his past, his techniques, the secrets of the world and then training training and again training. The illusion might have been a bit too intense for obito, or madara made it that way on purpose, so that obio would begin considering himself madara, while retaining his base memories and motivations. Like this, he would be able to play Madara's role in the best way possible. In other words, Madara fucked up his mind pretty intensely, making him into a miniature of himself, with improved skills and inplanted knowledge, in other words: the perfect vessel to carry on his plan.
Add: Yes Paul, i think what tobi has told us till now were all lies:
-I am madara uchiha
-I gave nagato the rinnegan
-I'm taking back what is mine
-The rinne tesnei was supposed to be used for me
He's acting. His whole mission was to act as madara until the plan came true. As to the "they were mine to begin with" that he said around Kabuto, there are 2 possibilities:
-everything madara had entrusted him, automatically became his. So the rinnegans were entrusted to nagato, but also to tobi to look after them, so they were his to take care of.
-or, madara's brainwashing was so intense that it made Obito lose the boundary between himself and madara and he really thinks he's the old uchiha leader sometimes.
2) Kisame has been very close to Tobi, I dare say on almost the same level of intimacy as Zetsu. Here's what I think about this: Madara Uchiha, the real deal survived long enough to control Yagura the mizukage and died somewhat in the middle of that mission. Simply put I'm saying that the long haired tobi and the short haired tobi weren't the same person. There were two Tobis, one was Obito and the other was Madara himself. The only thing Obito did as Tobi, was fighting Yondaime and setting the kyuubi free. The rest (like talking with itachi, controlling yagura) was done by madara before dying. At the time he was controlling Yagura, Obito was already his right arm, so I bet Kisame knew him in person as well. He was aware of the yagura plan. I think madara, before dying entrusted the rest of the plan to tobi/Obito, as well as the task to use his identity as his own. Like this Obito would become the "mizukage" for a bit too, and Kisame would recognize him in the hideout.
To make you understand betetr how i view the timeline of madara's life/death I'll make it in points:
-Madara defeats hashirama and steals his Dna
-Madara awakens Rinnegan
-Madara gives his rinnegans to Nagato.
-Madara replaces his eyes with some random ones.
-Madara spies on the uchiha clan and Obito
-Madara saves Obito, and orhestrates rin's death
-Madara and Orochimaru create zetsu
-Madara recruits Obito and indoctrinates him.
-Madara makes Obito attack the leaf as a proof of loyalty and to capture kyuubi
-Madara plots with itachi
-Madara takes control of Yagura in the meantime
-Madara dies, leaving the rest of his plans to Obito
3) In my opinion, every character in narutoverse has his own talent.
-Sasuke is a genius uchiha in ninjutsu
-Rock lee is a genius of hard work
-Neji is a genius with byakugan and Hyuga style
-Kakashi is a genius in his own way
-Tsunade is a genius healer, like sakura.
-Naruto is a genius of kage bushins.
Everyone is special in their own way. They may suck at everything else, but there is always something that makes them exceptional. What if Isay Obito is a genius with his sharingan? Zestu once said: "The sharingan is only a tool, it depends on the users ability to use it". Obito, who sucked at ninjutsu and ninja skills in general has finally found his strong point: his awakened eyes! From the moment he got them, he became a different person. No more crybaby, who must be protected, but a ninja who protects others and immediatly is able to use his strong point at his advantage. Then he unlocks MS (which i said over a billion times, is unique and hax. it can turn a weakling into an untouchable divinity). Assuming he had talent with sharingan, even his way of using it would be genial, making him someone totally different. Then he got hashirama cells, that gave him a boost in stamina, and probably enhancng him physically! Just look at how the zestu from slim and weak, became strThis would eong and full of muscles. This would even allow him to spam his MS without going blind. Add some training from madara, and the knowledge he might have given him about uchiha techniques and informatios...he would become quite formidable imo.
4. Tobi had MS at that time, even though it wasn't shown...but he had MS, so he could have controlled Kyuubi. Every uchiha with ms could have done that. It doesen't require anything more than a special genjutsu cast by MS.
The question about madara is already answered. You could be wrong assuming the yagura incident was been happening at the time where obito's not been born yet. It could have very well happened after the uchiha massacre.
i hope you enjoy