@tohoma: I agree Shisui's Kotoamatsukami could work, but it takes time. In that time Kakashi speed blitzs them like he did with Kaguya.
It only takes time to prepare after its been used. I'm assuming that in this battle Shisui hasn't used the technique for a decade. Also when did Kakashi blitz Kaguya? I only remember him catching her by surprise by phasing through her attack.
Sasuke was able to resist genjutsu with no MS, can't see why someone as powerful as Kakashi with MS couldn't do the same.
One Sasuke specifically trained his sharingan to resist Itachi's MS. Second even if Itachi's genjutsu wouldn't work on Kakashi Shisui's would most likely since Itachi expected it to work on Sasuke's perfect EMS who would be more far skilled in genjutsu than Kakashi.
@noone301994: what are Shisuis genjutsu feats against other MS wielders? Itachi has none.
Itachi assumed that Shisui's genjutsu would work on a perfect magnekyo sharigan in the series. He states that he anticipated that Sasuke would implant his eyes and when it happened Kokoamutsakami would be cast on him.