Itachi wins mid difficulty at best, Madara or Kaguya is a better match up..
He absorbed Sasuke's CS powers so he has Senjutsu. Juubito's attempts at cqc get swatted due to the fact that Itachi can best him via crow clonea, Katon variants like Crimson Flower Shuriken and Katon: Goukakyuu no Jutsu which will undoubtedly roast Juubito's weak body. That or he sends a Kunao right through Juubito's eyeball. He also has Ribcage variant in cqc, meaning he gets pummeled by it's superior strength and allows Itachi to tank everything.
- Yata allows Itachi to tank all of Juubito's attacks, and his Totsuka allows him to absorb Juubidama or the tree itself, which he can do two things from here, a) Shoot the absorbed Juubidama out the tip of his blade or b) absorb the tree's life energy and ascend to god level.
- Juubito in the end, gets bested by Itachi's superior speed and tricks, he gets feinted by a crow clone, followed by Katon Goukakyuu no Jutsu and than his real body pops behind him and Totsuka blitzes him, that or he just throws his Yata in a Frisbee like motion and beheads Juubito and just burns his body with Amaterasu, calling it a day.