Minato might have had a high level of intelligence, but he did not have Hashirama's Mokuton techniques, which could suppress the Nine-Tails. What sort of techniques could Minato possibly create to keep the Nine-Tails under control?
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Apparently both pieces of the puzzle are needed to fully control the Nine-Tailed Fox: "the powers of both Uchiha and Hashirama." Well, now that Sasuke has his own Eternal Mangekyou Sharingan, it will be much harder for Naruto to defeat him. Now that Sasuke's Mangekyou techniques are fully developed, the fight will become much more interesting. Of course, Naruto has made extraordinary progress as well in the past, so it will be interesting to see what powers he will develop as well. Yes, Minato planned ahead, but once again I ask, why did he not kill Madara if he could, and seal the Nine-Tails in himself, killing himself along with the beast? Also, Minato did not figure out Madara's identity - he simply asked Madara if he was "Uchiha Madara," to which Madara gave no definite answer. And as far as Minato defeating Madara, that is still all speculation, so we don't know about that yet.
I did not say the Eternal Mangekyou Sharingan makes one invincible, all I said was it is also effective for controlling a tailed beast, a valuable asset for the user. Amaterasu and Tsukuyomi, with the right planning, can be avoided, but Susanoo, as a matter of fact, does make the user invincible, if it is completely developed. The Susanoo that the Raikage destroyed was incomplete, so yes, the incomplete version is susceptible to harm, as shown below.
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Naruto has enormous reserves of chakra now that he has control of the Nine-Tails, and we can expect to see some impressive techniques from both sides in the future. After all, it's going to be the biggest battle in the entire series, the one that everyone has been waiting for.