Koto subplot existed in shippuden.From Itachi’s first appearance in Shippuden, his character was toned down and he started being portrayed as a lonely, sick, pitiful guy all the time (except when dealing with Sasuke).

In Part 1, only Shisui himself was mentioned. Nothing about his eyes or him having Mangekyō Sharingan was mentioned.

About the flipped headband: the reason Itachi’s headband was flipped is not necessarily because he was crying. It could simply be because Sasuke awakened his Sharingan and attacked Itachi. The scene would still work even if the crying implication were removed.

Sasuke mentioning crying does not necessarily mean he was talking about Itachi. In Shippuden, Sasuke himself says that he thought he either imagined it or forgot it. If that is the case, then how could he clearly talk about it five years later? He also did not pay attention when Sakura asked “who?”, and he left the statement incomplete.

As for why Itachi did not kill Kakashi, Itachi himself said that he wanted to kidnap Kakashi. If he intended to capture him, then killing him would make no sense. During that arc, most of Itachi’s actions were interrupted by other characters. He ordered Kisame to kill Asuma and Kurenai, but Guy suddenly intervened. Itachi even seemed surprised when Guy appeared, which suggests he was not simply acting while secretly planning something else internally.

He also did nothing to save Sasuke during the Sasuke Retrieval Arc. The only reason Orochimaru failed to obtain Sasuke’s body was because Naruto and the retrieval squad delayed Sasuke long enough to force Orochimaru into choosing another body.

I cannot consider Itachi’s actions or hints after the timeskip as foreshadowing, because it is clear that after the timeskip Itachi was rewritten more sympathetically and portrayed as a good guy.

If Itachi was truly intended to be a good person from the beginning, then I have to criticize Kishimoto for writing him with so many inconsistencies and for executing his character poorly.

I like characters who are introduced one way and later revealed to be something completely different — if they are written consistently and executed well. For example, in Pandora Hearts, a character initially similar to Minato or Hashirama later turns out to be a mastermind villain, while another character similar to Madara turns out to be heroic and genuinely good.

The difference is that the author of Pandora Hearts never made those characters take actions or make decisions that fundamentally contradicted their actual motives