ok, here are my thoughts...
itachi
itachi is not back as a human being. he still is a zombi, not having his real body, but the body of the sacriface made for the IWR. So there is no way for him getting back to normal.
the question is if now that he broke free from kabutos control, is kabuto still able to just end the technique, resummon him and then he is being controlled again? or do we have an immortal itachi, who can use his eyes again on the side of the JSA? would be cool
Shisuis eye
itachi said, you need the chakra of hashirama, not the chakra of somebody related to him. so tsunades chakas won't work, neither that of naruto because he is an uzumaki and distantly related to the senju...blablabla. it has to be the chakra of the first. so either the cells that madara obtained or yamato. but as itachi must have known of yamato, i guess he would have considered that possibility. anyway, naruto will find a way to make the eye work again, otherwise kichi would not have mentioned that possibility
about shisui having ms... we all know that there is an other way to get ms, besides killing your best friend-> kakashi. but as itachi wanted sasuke to do so, i think it must be something that itachi thought sasuke would not be able to do. i got no idea what that would be, but i think kakshi and shisui both got their ms that way. maybe your best friend dyeing is enough. although i got no idea who that could have been in kakashis case.