Okay, so that's why he killed his entire family (with the exception of Sasuke and Obito) for the sake of the Leaf, and because he was ordered to. That must also be why he programmed Shisui's eye to make Sasuke "protect the leaf", and even if that failed, it was still his original intention.
either kishi wanted us to believe he was evil or maybe itachi wanted to show kakashi his powers so that kakashi knows the extent of itachi's genjutsu abilities and thus trains to be prepared enough in case they meet again....
do what the **** makes you happy, cause at the end; who's there? you.
Re: Why did Itachi use Tsukuyomi on Kakashi?
The answer is above but because since Kisame is an Akatsuki member so itachi had to make a scene for it to look he doesn't care about the people of Konoha but he actually trying to help and he cares for his brother Sasuke.