You talk as is if Itachi even intended to counter KA. No he was caught by his own jutsu intentionally. He himself knew he was under the genjutsu(KA), didn't he? Sasuke on the other hand doesn't even know the jutsu, so how could he prepare himself to counter a genjutsu he doesn't know and couldn't even be aware of if it ever happened?
Now answer me this:
- There is a disturbance in the chakra flow when KA is used, isn't it?
- Ao noticed the disturbance in Mifune's chakra flow when KA was used on him, didn't he?
- A skilled sensor can notice the disturbance in his chakra flow, can't he?
So what stops him from noticing if he is even caught by KA when he has already shown the capacity and even told he can't be fooled by the technique?
Itachi said that Genjutsu
don't work against someone who has the same eyes, yet Itachi was controlled in the long run. Kotoamatsukami is not just a Genjutsu, it rewrites your mind. Therefore Kabuto was forced to lay a new mark at Itachi, in order to take control over him again. Danzo didn't want to give a command to Mifune, he just wanted to control him for the period of the Kage meeting, and Ao, an outsider noticed the disturbance of the ones chakra, who was controlled. Ao himself said, that Shisui controls his victims without them noticing it, he would contradict himself if a sensor could indeed notice it. It means, even if you know your opponent uses Kotoamatsukami, you cannot tell whether and when he uses it on you, you simply can't recognize it by yourself as you believe the control being your own mind. And if Kotoamatsukami gives you a command, it rewrites your mind to the extent to make this idea being your own. Again, he wanted to control a user of the EMS, though Itachi stated, that Genjutsu against someone with the same eyes
is not working. Further he wanted to do it for the long run, forever, making Sasuke an ally of Konoha. This would be a bit erroneously, if this would be an illusion that constantly holds you in an illusion, where you can be freed if someone disturbs your chakra flow, isn't it? Even when Itachi was caught by Tayuyas Genjutsu, Sasuke freed him from it but the control of Kotoamatsukami was still holding. Again, it isn't just an illusion, it rewrites your mind and makes this command being your idea.
The facts are against you, clearly against you.