If you look at Kakashi when the 9 Tailed Fox attack occurred, he looked much older. His body resembled more of a grown man than a teenage boy. So Obito could have looked the way he looked when the attack happened. Also, when you are trained by Madara Uchiha, you can advance very rapidly. Look at Naruto's and Sasuke's progression in such a small time. The second eye can be explained very easily, he stole it. He had plenty of eyes thanks to the Uchiha massacre. The next question is: why cover it up? Same reason Kakashi covers it up...He probably can't turn it off and it takes up too much of his Chakara. He cracked his mask to use it when he really needed it. I know Uchiha are supposed to be able to do this, but maybe he can't, because he only has one eye or some random explanation like that. Last question: why can he have Rinnegan out all the time? It probably doesn't have the same affect on the chakra like a sharigan does.