Oh..this is awesome, here we go.
Okay Let's see, we know that Tobi knows Madara, so if indeed it is Obito, he's had like 3-6 years of training by Madara. Remember now, Sasuke had 3 years of training with Oro, and could arguably have beaten Kakashi (Though I have no doubt that he could, just don't want to start a meaningless debate) at the finish of his training.
Now this is Madara, a mastermind. One who achieved the rinnegan, tricked the entire ninja world into believing he was dead, and even planned to be resurrected later in the future. Spending even a year with a mastermind like this could prove very beneficial for the student. Also, let's not forget that he too is a sharingan master. Obviusly so since he achieved the rinnegan. Obito is an uchiha himself, certainly this relation between the two would have a more resulting benefit than the Sasuke and Orochiramu student/teach relationship.
Another thing, what most overlook in that fight, is that Tobi used one tech, or maybe two. What I'm saying is don't judge the skill of a character based on one powerful tech. That tech is the only reason why the was able to go up against Minato, take that away from him, and it would have been the same as a "kid" Obito. He simply has a convenient ability.
In short, you can't really judge that fight with the Obito that Kakashi knew. Not when he have been a student under Madara, and had one heck of a convenient tech, and only used that one abilty throughout the entire fight.
There's also no proof of Madara being dead around this time. You know what I find strange? The edo tensei is said to resurrect you the way that you died. Yet Madara was resurrected in a young looking age. He looks the same age he did as when he fought Hashirama. Now, we know that he lived on to meet Nagato. But why doesn't he look any older? No matter how you look at it, it's odd. If Madara lived to be old, but then Kabtuo "improved" him (Though there is nothing suggesting an improvement on his age), Madara would have no doubt found it strange that he wasn't in an old body, especially since he was expecting to be brought back by Nagato.
That's another odd thing, why live to become an old man, and then desire to be brought back in that same condition. We know that Madara has planned a lot, and thought of a lot, and he knew a lot. I actually believe that in his dying times, he was able to transfer his "energy" or "lifeforce" somehow into Obito before he died. So that he would be resurrected in his "prime". And this transfer increased the age of Obito. I know, lots will call it farfectch, but meh xD
Anyway, who's to say how long Madara lived when he should have been dead before Nagato was even born. I don't know the age differnce between Madara and Onoki, but I do know that Onoki was in the same era as Madara, and he's still alive. And if you subtract the Naruto's age which is 16 years, and the age difference of Kakashi when he was a teen compared to when he was a kid. And you're probably gonna end up with like 20-30 years. Madara could have done it with Senju cells if Onoki could pull it off.
Now we can't just take away the fact that Tobi rolls with a guy named Zetsu. Yeah you're probably saying, "Oh there he goes". Just bare with me, we know that one of Zetsu's abilities is regeneration. No matter what you cut off, he can regenerate it. We see that it appears that Tobi himself has pieces of Zetsu in him. You CAN'T just overlook this. Obviously there's a reason behind this. What else do we know that Tobi has, Senju dna? This implies that his body has been severely operated on. I mean what would happen if parts of Zetsu was to take over someone's body? No one really knows. But aging shouldn't seem too impossible when someone's body consist of so many unusual DNAs. Heck, kabuto just had the freaking sound 5 come out his body. There's already so many strange things in this manga.
And there's clearly an "aging" issue with Madara. Which I already mentioned. It basically proves that age-manipulation is indeed possible.
This can be countered with the fact that half of his body would have been badly damaged in the incident. He may not even remember who he was anymore. Not to mention potential brainwashing from Madara.
I know some of my points are based on assumptions. But when you view it objectively and with an open mind, you'll see there's a "possibility" that Obito's body may be involved.
Note: I also find it very interesting Kishi has decided to put Kakashi there with Naruto when Tobi may reveal his identity. Like I said, I think there's a great possibility that it will turn out to be Obito's body at least.
To add to this old post of mine, one of the biggest arguments aside from Obito being crushed is tha the timeline between Madara and Tobi working together doesn't match with Obito's timeline. What readers fail to see however is that Kishi never gave any solid proof as to when Tobi and Madar actually met. There's absolutely none...
Another argument is why would Madara choose a half dying kid to ressurect him? It actually makes perfect sense that he would. If he was able to brainwash Obito with his own ideals throughout his earlier years, mentor him, and then place Zetsu there with him after he's gone. Then trusting a kid whose been trained to follow your way is much more guaranteeing that trusting an adult whose already mature enough to have his own view of how the shinobi world should be.
I mean one miscalculation in their character and ideals, and he's not being ressurected...
I'm almost certain Madara thought of this.
And then there's the bigger issue of Obito's death. Miracles happen even in real life though, people living with disfigured body parts because of terrible accidents. I don't know why it's so impossible to believe that it's possible in a manga lol. Especially when there' a tech like the rinnegan.
Well that's all. ^^ Though I'm slowly developing another theory (Obito and the elder son involved) but have to think on it some more.
Okay, thought about it, and here's what I came up with.
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THEORY 2
Tobi is indeed the elder son, but is using Obito's body. Okay, Madara took his brother's eyes and gained EMS, and then went back to read the stone. But what he saw was more than details about the Sharingan left by the so6p, he saw something the elder son left himself, the details on how to ressurect him and his aid in th reader's quest for more power. Afterall, anyone who has obtained the EMS and seeks further knowledge by reading the stone is without a doutb seeking more power. The elder son knew this, and used it to guarantee his return.
But he came back "incomplete", in other words he was very weak, and paled in comparison to Madara's strength...
However, he had a rinnegan of his own. They came up with a plan (I will mention later), this plan involved the creation of Zetsu. Anyways, he told Madara he must have a near death experiece. But Hashi actually KILLED Madara, afterall, it's unlikely that Hashi wasn't sure that he was dead. What he didn't know...is that the elder son was alive and possessed the eyes we know as the rinnegan. The elder son ressurected Madara, but he couldn't have done so without consuming lots of chakra from an already weak body (or whatever the heck he was). So Zetsu, who can replenish chakra was created from an experiement on how "Tobi" (Getting tired of saying elder son) could survive the depletion of chakra as a result from using the rinne tensei.
After this, Madara had the rinnegan which he unlocked just before he died. He either consumed hashi's cells ro lived naturally. Anyway he lived to meet Nagato, this boy was just perfect, he was an Uzumaki who possessed lots of chakra. And since Tobi wasn't in the condition to actually handle the rinnegan, he passed it on to Nagato.
Tobi and Madara then planned for Madara's ressurection later, but there was something Madara and Tobi had to do, get Tobi a more suitable body than what he had...
This is where Obito comes in at, Madara then used his own rinnegan to revive Obito. And some unknown technique was used that allowed Tobi to enter his body. Depending on the effects caused by this tech, Obito may have aged from this, Madara then passed on. And then Tobi makes his attack (along with his new found techs from obito's sharingan) on the Leaf.
Haha, it's just a theory.