- Sharingan helps to track movements. One tails Naruto was blitzing Sasuke so badly that he couldn't react despite 2tomoes, but when his 3tomoe sharingan appeared, he wasn't only capable to follow, but counter Naruto easily. That particular example clearly shows the advantage Sharingan can give to a Uchiha, so it's a factor you should take into consideration. In Uchiha's case, speed is not necessarly involve. Their eyes are capable to track movement speed to some extent, except from high shunshin users like V2 Raikage, Naruto and Minato. Unorthodox styles like Bee eight sword's style are also capable to surprise their Sharingan reading skills, like it also does happen when they are attack from their blindspot, like they also can't read chakra manifestation like it's shown during the fight between Sasuke and Naruto at the VOTE
- Naruto despite KM, still has poor taijutsu(3.5). KM only increases his overall power and speed, not his skilfulness in taijutsu. Actually SM for example is better than KM in this perspective. In mid air battle like it was the case in the manga, there is no support to actually use decent speed. It only involves taijutsu in that particular case, and Naruto is far from the best at it, so it actually even downgrade Itachi's performance there for not being capable to take advantage against a 3.5 in taijutsu
- Naruto was also near end KCM. He already dispatched his chakra into more than 20clones, so with the chakra he had back then, he could not use many moves. Reason why after a small battle against Nagato, the chakra directly ran out
- Naruto was also fighting with no intent to kill
Not trying to downgrade Itachi here, since he is actually fast, but i think we should try to put things in their context U_U
