Yoru, For Tobi to be Obito,

1_ He must have survived the rock fall

2_ He must have entered a time machine and grown older than Kakashi when he fought Yondaime.

It makes more sense that somebody took Obito's other eye. But If he is entirely made of Zetsu parts anyway, and his head is filled with Madara's knowledge and skills, then none of this matters at all.