It makes sense, honestly. The only reason Obito hasn't taken out Madara and Sasuke yet, might be because he is to busy taking care of the Alliance and the plan. If he succeed in his plan, he will only have to worry about Sasuke and Madara if they are able to counter it. Also, I saw someone mention that you can counter the Genjutsu by not looking at the moon, I think this is wrong. As I do think that the Infinite Tsukuyomi affects all the senses of a person, not just their eyes.
I think its more likely that a Jin. can counter the Genjutsu. ( Which is something they didn't plan with, since they planned that all the Jin.s would be gone by the time the plan got to this level.