@NeedleJizo. Sasuke wins this, if Shisui does not have Koto. Sasuke's speed have been mentioned many times, able to dodge Raikages punch, and Killer Bee's attack. Dodging bombs near the second they explode. Sasuke is fast, he's just wasn't born in the time fo war to be mentioned of it, I would say, he's way faster than Shisui.
Genjutsu skills, well Shisui was famous for it, but Sasuke also withstood Itachi's basic Genjutsu and as well as break out of Tsukuyomi.
And about the Danzo fight, while Danzo was holding back his said powers. Sasuke came after fighting Kages, Samurais and gaining pain even in the cells because of Susanoo. The only healing he got was from Karin, who even after healing Sasuke with her special ability, worried about him using Chidori, since he's still injured even after being healed by one of the best healing techniques in the series. And whatever Chakra Danzo held back, wouldn't matter. Since the whole theme of the fight was Sasuke killing off Danzo(and thus reducing his Sharingan), so even if Danzo held back, he was still tricked into believing he had held back some power(His sharingan for example) only go realize that it was a genjutsu. The fight was of who's gonna get killed faster and not who's chakra gonna last out, so even if he was holding back his power, it wouldn't change a thing. Period.
So with mastery with sword, shurikens and taijutsu, a close combat battle wouldn't be good for Shisui.
And with Kirin, chidori(And it's variants), Amaterasu, Susanoo, Taijutsu, mastery with weopens and snake summons, Sasuke takes this.
One thing before I end this, MS Sasuke has grown stronger than Shisui, it's a fact, agree or not, but if Shisui has his Koto then he might very well defeat Sasuke, since the Koto is another unexplained OP jutsu like Itachi's TB. Without any clarifications of it's weaknesses or why it didn't make Shisui the strongest shinobi ever.
This is just my opinion, though.