I responded dude, on the other page. Mangekyo Sharingan does use the different eye's, it also happens that Kakashi uses his left eye also for Tsukiyomi, probably meaning that hoping he will be able to do Amaterusa* (spelling) is wishful thinking.
As for the Yondaime's secret jutsu, it probably is a "cannot be copied" jutsu. But he probably just applied hardcore shinobi logic to create that jutsu. The same way he thought up rasengan. It cant be akin to bloodline limit, since he isn't actually doing ninjutsu. I got the impression that his understanding of summons allowed him to figure it out. Basically, because the summons (Enma, that frog) aren't actually a part of the naruto world as we know it, they have to be part of another dimension. He figured out a way to manipulate a link between both places. but then again, I could just be talking nonsense.
Bloodline limits have to start somewhere, its possible that genetic mutation in a person brings forth a new bloodline limit. Or the bloodline limit is latent in shinobi, and only those with the necessary ablity are able to "awaken" it. Like every Uchiha was sharingan, but not every Uchiha was the ability to use it. Now imagine two whole generations of n00b Uchiha's who cant activate sharingan, the ability will seem to die out, then one guy manages to activate it in the third generation, it would appear that he has a special personal ability, which isn't completely true.
♥ of the cards!
No matter the genius, they all fall to mediocrity in front of the Uchiha!