You've made some good points, but the truth remains that Tobi's real identity is Madara. But it is very likely that Tobi stole Obito's right sharingan after or right before Obito was killed.
In Manga 502, after Minato says it can't be Madara because he's dead, Tobi says" Oh...I don't know about that". This doesn't isn't Madara, Tobi's just playing into the suspicion the Naruto series is known for. When Tobi refers to the "plan both for war and for peace" he's talking about the Eye of the Moon Plan. Madara's plan is to gather all the tailed beasts in order to fuse them back into their original form, the Ten-Tailed Beast. He will then become jinchuriki to the Ten-Tails giving him immense power and the ability to project his Mangekyo Sharingan on to the moon. He intends to use the moon, the prison of the Ten-Tails body, to cover the world in an "Infinite Tsukuyomi", thereby letting him control every living being, creating a world in which no war or crime occurred. This is something only Madara Uchiha would be capable of knowing and of doing.
In Manga 241 after Kakashi decides not to go after Rin, Obito says “I will destroy that so called idea of a shinobi". I guess you could say it hints at a more malevolent side Obito. But remember, it was the spur of the moment. He said it out of annoyance towards Kakashi's uncompassionate attitude. It's not surprising that Tobi knew of Minato's fighting style. The 3rd Great Shinobi war was just the year before and Minato's feats, including defeating an entire shinobi army on his own, earned him the title "Konoha's Yellow Flash". His fighting style was known throughout the shinobi land. As for when Tobi went for Naruto, what did you expect him to do? A man just threatened to kill his new born baby boy. Most people would react the same way, especially someone like Minato the Hokage. Regardless of whether Obito was Minato's teacher, Tobi knowing Minato's fighting style isn't surprising. Yes it is true, both Kakashi and Tobi can control time and space jutsu. That's where the question of whether Tobi stole Obito's sharingan comes into play. I think he may of stolen it, just like Danzo stole Shisui's, and many other Uchiha's, sharingan. This would explain why Tobi can use time and space jutsu.
You mixed up which sides were which making it very confusing. You’re calling right side left and left side right. Obito gave his left sharingan to Kakashi, not his right. Tobi only reveals his right sharingan not his left. Do you watch the mirrored Naruto episodes? Anyway, after Obito gave his left sharingan to Kakashi, whose left eye was injured earlier in a fight, Obito is left in the rocks with his right sharingan, which Tobi supposedly stole.
Again, it was Obito's entire right side that was crushed, not his left. I'm not sure Tobi ever removed any of his limbs. Where in the manga did he do that? And if Tobi has any injuries at all, they were sustained from his battle with the 1st Hokage.
When Konan injured Tobi allowing some of his mask be blown off, you saw a piece of Tobi's face:
This is the same eye structure of Madara in an earlier manga chapter:
Now this is very similar to Madara's eyes not Obito:
Madara's eyes were much more slanted than Obito's, while Obito's is more square, as you can clearly see in these pictures. And you can also see the clear wrinkles in face. You can't mistake obvious wrinkles for scars. What Kakashi has on his left eye is an obvious scar, what Madara has under his right eye are obvious wrinkles. If it was Obito, he wouldn't have these wrinkles.
Another thing is how fast Obito grew. He couldn't have grown to the size of Minato in just one year. That also gives him one year to unlock the Mangekyo Sharingan, become an elite ninja the types of which Minato had trouble with, and figure out how to control the Nine-tails.
And if Tobi is Obito, why would he of killed off his entire clan? For what? He had no reason to. And that would also mean that Obito gave Nagao the Rinnegan, as said by Tobi in Manga 509. Obito was probably younger than Nagato during the 2nd great war, if Obito was even born at all, which makes it impossible for him to of given Nagato the Rinnegan. Tobi could be lying, as he often does, but as for now it’s yet to be proven false.
I think the person Kabuto awoke was Izuna Uchiha, Madara's brother. That's probably why he reacted like that. It's just a possibility I have no proof for.
I can't edit my answers for some reason, so if you have anything else to say send me a message.