So, Itachi's plan when he entrusted his crow to Naruto was when Naruto encountered Sasuke in a battle after he had implanted Itachi's MS to awaken the EMS, the crow would exit his body and cast Kotoamatsukami. Of course, this did not happen in the canon storyline.
I would like to discuss the changes that could and would have happened if Itachi's plan had succeeded.
Assuming Sasuke fought Naruto directly after he got EMS ( As he swore that he would kill Naruto, once he gets Itachi's eyes in the chapter where Naruto encounters Sasuke, Sakura and Kakashi ), Sasuke most likely would've come on Naruto's side directly and supported him in Fourth Shinobi War. Probably, the final Naruto vs Sasuke ( And Sasuke's revolution wouldn't happen ).
Another thing is, I don't think Sasuke and Naruto would've gotten their Six Paths powers and Rinnegan. They would only have EMS And BSM at max.
Well, I doubt it would have changed much. It could've had the opposite effect in fact. Koto is powerful and all, but once the target is aware they are under it's effects, they are seemingly able to dispel it. A reference to this is Mifune, once he was aware of Koto being used, he realized his actions.
What would have likely happened? Naruto and Sasuke would have fought, Sasuke activates EMS, crow pops out with Shisui's eye. Sasuke wouldn't know the ability but he would expect some sort of visual jutsu arising from the MS. Koto would land and it would compel Sasuke to "protect the leaf".
However, Sasuke would still try to deduce the mechanics of the MS that just appeared. He would eventually concluded that genjutsu was used. Thus, the effects of koto would be negated. Once this happens, it would further enrage Sasuke as it is another action that Konoha "forced" Itachi to do for the sake of the village.
I guess this plot would only happen if Itachi never was returned back as an edo. Then it would lead the world to face the endless edo tensei jutsu and such, so it may better to imagine that there's no war happening, or just Kabuto not in it.
Sasuke meets Naruto, they stare down with each other.
Sasuke: Okay, Naruto. Just as you asked, I came for you first. Then after I kill you, I'll burn down the Leaf!
Naruto: Sasuke, I know you're doing this for your brother, but the people at the Leaf, they didn't do anything!
Sasuke: Their ignorance over Itachi's sacrifice, their laughter after the deaths of the Uchiha, their scorn on Itachi, even after what he did for them! I'll make them all pay for it! I'll kill them all! Starting by you, Naruto!
Naruto: A new eyes? *Naruto starts to choke, while feeling something coming out of his mouth. Gets shocked over a crow coming out of his mouth.*
Naruto: What the?! What did I ate for lunch today?
Sasuke spots an MS over one of the Crow's eyes*
Sasuke: That Sharingan?!
Gets controlled by the genjutsu, then becomes the slave of the Leaf as Itachi wanted him to be.
Naruto: What did just happen? Where did that crow come from? And why did it have a Sharingan in it's eye? Wait, was it genjutsu?*Looks at Sasuke, who isn't moving and has his face over the ground.* Ah, forget about that, I have more important things to worry about.
Sasuke remains silent.*
Naruto:Hey! I don't have a whole day, you know! Are you coming at me or what? Got scared by a crow? Or was it your genjutsu?
Sasuke remains silent.
Naruto: Somethings wrong. Hey, Sasuke are you alright?
Sasuke turns his head up, stares at Naruto.
Sasuke: I will. Protect the Leaf.
Naruto: Huh, what the? Where did that come from?
Sasuke: I will protect the Leaf no matter what, as my brother, Itachi did.
I just imagined the conversation to be like this or something like this. In the end, Naruto brings Sasuke back. Sasuke thus starts on the side of the five village.
Sasuke being caught by Kotoamatsukami would've happened only if Naruto hadn't met Edo Itachi. But in that case, with Itachi and Nagato roaming around the battlefield, the Allied Forces would've been screwed. Kabuto summoned Madara only after losing Nagato and Itachi, which hints at how highly Kabuto thought of them. Being reanimated, Itachi could spam Tsukuyomi, Amaterasu and Susanoo, while Nagato could create stars left and right. That's a pretty dark scenario for the good guys (Itachi even commented on how the two of them together were almost omnipotent).
Back to the topic, Sasuke would've fallen for the genjutsu hook, line and sinker. Even if he himself noticed that something was amiss, he wouldn't be able to do anything about it. A genjutsu that overwrites even Kabuto's control of Edo Tensei is that strong. It would've been funny to see Sasuke screaming "I'll kill you" and then say "I'll protect Konoha".
Well i can't say I entirely disagree with the others as far as the Kotoamatsukami not changing much, since despite Itachi’s best efforts and best intentions the events that lead up to the fourth great ninja war were the doing of Obito (acting on Madara’s behalf who himself was a puppet of Black zetsu). That being said I do think it would have made the series both shorter and considerably less interesting. After all if the kotoamatsukami had worked on Sasuke and instilled in him as strong a desire to protect the Hidden Leaf as Itachi possessed then he would turned against anyone who threatened the Leaf. That being said Itachi's crow (by Itachi’s own admission) would only emerge if Sasuke activated his Eternal Mangekyo Sharingan in Naruto’s presence. Naruto was strong enough after defeating Kaguya to force Sasuke to do so but before that time (and almost certainly before having master Kurama’s power) Sasuke was still the stronger of the two of them, not by much but by a big enough margin that he wouldn’t have had to his full visual prowess. Plus it occurs to me that even if Itachi's plans worked the plans of the Akatsuki were too far advances to be much more than slowed down by Sasuke's making an about face. All in all while Sasuke changing sides sooner might have made some difference he and Naruto still would have ended up in the same situation they eventually found themselves in. Besides given that after the fourth great ninja war Sasuke adopted Itachi's mission in life (protecting the Hidden Leaf) and atoned for his many crimes I don’t really think his having done so earlier would have change a commensurate difference.