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This links to a thread I made a while back which explains this in full detail.
Now, to start, let me explain that I am not saying anything with certainty but rather making an assumption based on some 'evidence' I stumbled across.
I am making a point that when Kisame comments on Madara's ability to use his Sharingan to control the Sanbi's host Mizukage, his comments make it 'seem' as though a sharingan alone cannot simply control or catch a Perfect Jinchuuriki and only a very unique person could manage this,even with Sharingan.
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We see that Sasuke's Tsukuyomi, which is far superior to any regular Genjutsu, had minimal effect on Bee, who was playing around in that fight.
Here's Bee's explanation of how he Beasted and nearly killed Sasuke who used Tsukuyomi, the 2nd best form of Genjutsu.
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So, what I am getting at, is that a Sharingan user cannot use Genjutsu to control a Perfect Jinchuuriki. Unless they are someone who has an incredible mastery of Genjutsu, such as Itachi,Madara and Shusui.
Note: I am not saying Itachi nor Shusui could but rather that they were the sort of level that a Genjutsu user would need to start control of P.J.
Conclusion: Sasuke won't be able to control Kyuubi while Naruto & Kurama are cooperating.
I feel there are a few more issues I need to point out.
Sasuke's EMS:
It has all of Itachi's abilities 'apparently'. So some of you will assume his Tsukuyomi can control a Perfect Jinchuuriki. That isn't the case as far as I'm aware. I'll explain.
1: Itachi & Kisame had to fight all the Jinchuuriki they came across. If Itachi were able to control the Perfect Jinchuuriki, he would have done so then & avoided a fight.
2: The user cannot move while using Tsukuyomi as far as I'm aware. I may be wrong, but Itachi never moved while using it.
3: Itachi's Tsukuyomi only lasted 3 seconds in the real world or 1second=24hours in Tsuku, but this gives the user a very small opening to attack the target in the real world and plenty of genjutsu time for the host & Biju to undo the technique.
Adding Koto Amatsukami thoughts:
1: Koto Amastukami still(as far as we know) only casts the Genjutsu on one target.
2: The Perfect Jinchuuriki, are two people/entities.
3: If a Perfect Jinchuuriki has Koto Amatsukami cast upon them, be it Biju or Host, the partner should still sense the Genjutsu/chakra flow disruption and break the other free.
For these reasons, I feel K.A is out. Again not saying it for sure, just using some thought.
Lastly a little pointer about Sharingan & Uchiha:
1: When Kyuubi attacked the village, if the Uchiha had the power to control him, they would have stopped him right away. They were an entire clan. At least a few should have been able to get to the field and stop him.
2: Of all the Uchiha clan, not a single member seemed able to or attempted to control the fox when it attacked and they were Konoha's Police force. This is enough for me to believe that 90%+ of Sharingan users/Uchiha are unable to harness the power to control Biju.
3: Remember that at this time, the Uchiha were not thinking about starting a coop.
Those reasons tell me Itachi & Shusui would be unable to control a Perfect Jinchuuriki, they were still very talented Genjutsu users though. But they serve just as examples though.
Comments and feedback welcome. Thanks for reading.